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2e3ba8a9bf ... boundary-c

Author SHA1 Message Date
p.vanderwilt
2a520be33b Refactor measurement position assignment and update grid position calculation in Reactor classes to align with new generalFunctions 2025-10-10 11:27:55 +02:00
p.vanderwilt
baecf2f599 Functioning code, requires improved sequencing 2025-10-02 17:39:31 +02:00
p.vanderwilt
cd3a19e66f Fix boundary conditions for advection 2025-10-02 13:48:47 +02:00
p.vanderwilt
3aea0e55c4 Rewrite for improved boundary condition 2025-10-01 16:50:48 +02:00
p.vanderwilt
d9511dc3c7 Implement simple BCs 2025-09-30 15:36:25 +02:00
p.vanderwilt
993482f8c0 Deal with mulitple parents and set downstreamReactor for improved boundary conditions 2025-09-29 16:58:46 +02:00
p.vanderwilt
5f4ebdc2af Fix reference error and improve child variable naming 2025-09-29 15:45:07 +02:00
p.vanderwilt
6c79d0ef9b Use improved boundary conditions for upstream and downstream reactors 2025-09-29 15:34:54 +02:00
48 changed files with 3736 additions and 4940 deletions
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.gitignore vendored
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# Logs # Logs
logs logs
*.log *.log
npm-debug.log* npm-debug.log*
yarn-debug.log* yarn-debug.log*
yarn-error.log* yarn-error.log*
lerna-debug.log* lerna-debug.log*
.pnpm-debug.log* .pnpm-debug.log*
# Diagnostic reports (https://nodejs.org/api/report.html) # Diagnostic reports (https://nodejs.org/api/report.html)
report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json
# Runtime data # Runtime data
pids pids
*.pid *.pid
*.seed *.seed
*.pid.lock *.pid.lock
# Directory for instrumented libs generated by jscoverage/JSCover # Directory for instrumented libs generated by jscoverage/JSCover
lib-cov lib-cov
# Coverage directory used by tools like istanbul # Coverage directory used by tools like istanbul
coverage coverage
*.lcov *.lcov
# nyc test coverage # nyc test coverage
.nyc_output .nyc_output
# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files) # Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files)
.grunt .grunt
# Bower dependency directory (https://bower.io/) # Bower dependency directory (https://bower.io/)
bower_components bower_components
# node-waf configuration # node-waf configuration
.lock-wscript .lock-wscript
# Compiled binary addons (https://nodejs.org/api/addons.html) # Compiled binary addons (https://nodejs.org/api/addons.html)
build/Release build/Release
# Dependency directories # Dependency directories
node_modules/ node_modules/
jspm_packages/ jspm_packages/
# Snowpack dependency directory (https://snowpack.dev/) # Snowpack dependency directory (https://snowpack.dev/)
web_modules/ web_modules/
# TypeScript cache # TypeScript cache
*.tsbuildinfo *.tsbuildinfo
# Optional npm cache directory # Optional npm cache directory
.npm .npm
# Optional eslint cache # Optional eslint cache
.eslintcache .eslintcache
# Optional stylelint cache # Optional stylelint cache
.stylelintcache .stylelintcache
# Microbundle cache # Microbundle cache
.rpt2_cache/ .rpt2_cache/
.rts2_cache_cjs/ .rts2_cache_cjs/
.rts2_cache_es/ .rts2_cache_es/
.rts2_cache_umd/ .rts2_cache_umd/
# Optional REPL history # Optional REPL history
.node_repl_history .node_repl_history
# Output of 'npm pack' # Output of 'npm pack'
*.tgz *.tgz
# Yarn Integrity file # Yarn Integrity file
.yarn-integrity .yarn-integrity
# dotenv environment variable files # dotenv environment variable files
.env .env
.env.development.local .env.development.local
.env.test.local .env.test.local
.env.production.local .env.production.local
.env.local .env.local
# parcel-bundler cache (https://parceljs.org/) # parcel-bundler cache (https://parceljs.org/)
.cache .cache
.parcel-cache .parcel-cache
# Next.js build output # Next.js build output
.next .next
out out
# Nuxt.js build / generate output # Nuxt.js build / generate output
.nuxt .nuxt
dist dist
# Gatsby files # Gatsby files
.cache/ .cache/
# Comment in the public line in if your project uses Gatsby and not Next.js # Comment in the public line in if your project uses Gatsby and not Next.js
# https://nextjs.org/blog/next-9-1#public-directory-support # https://nextjs.org/blog/next-9-1#public-directory-support
# public # public
# vuepress build output # vuepress build output
.vuepress/dist .vuepress/dist
# vuepress v2.x temp and cache directory # vuepress v2.x temp and cache directory
.temp .temp
.cache .cache
# vitepress build output # vitepress build output
**/.vitepress/dist **/.vitepress/dist
# vitepress cache directory # vitepress cache directory
**/.vitepress/cache **/.vitepress/cache
# Docusaurus cache and generated files # Docusaurus cache and generated files
.docusaurus .docusaurus
# Serverless directories # Serverless directories
.serverless/ .serverless/
# FuseBox cache # FuseBox cache
.fusebox/ .fusebox/
# DynamoDB Local files # DynamoDB Local files
.dynamodb/ .dynamodb/
# TernJS port file # TernJS port file
.tern-port .tern-port
# Stores VSCode versions used for testing VSCode extensions # Stores VSCode versions used for testing VSCode extensions
.vscode-test .vscode-test
# yarn v2 # yarn v2
.yarn/cache .yarn/cache
.yarn/unplugged .yarn/unplugged
.yarn/build-state.yml .yarn/build-state.yml
.yarn/install-state.gz .yarn/install-state.gz
.pnp.* .pnp.*

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LICENSE
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Appendix Appendix
‘Compatible Licences’ according to Article 5 EUPL are: ‘Compatible Licences’ according to Article 5 EUPL are:
— GNU General Public License (GPL) v. 2, v. 3 — GNU General Public License (GPL) v. 2, v. 3
— GNU Affero General Public License (AGPL) v. 3 — GNU Affero General Public License (AGPL) v. 3
— Open Software License (OSL) v. 2.1, v. 3.0 — Open Software License (OSL) v. 2.1, v. 3.0
— Eclipse Public License (EPL) v. 1.0 — Eclipse Public License (EPL) v. 1.0
— CeCILL v. 2.0, v. 2.1 — CeCILL v. 2.0, v. 2.1
— Mozilla Public Licence (MPL) v. 2 — Mozilla Public Licence (MPL) v. 2
— GNU Lesser General Public Licence (LGPL) v. 2.1, v. 3 — GNU Lesser General Public Licence (LGPL) v. 2.1, v. 3
— Creative Commons Attribution-ShareAlike v. 3.0 Unported (CC BY-SA 3.0) for works other than software — Creative Commons Attribution-ShareAlike v. 3.0 Unported (CC BY-SA 3.0) for works other than software
— European Union Public Licence (EUPL) v. 1.1, v. 1.2 — European Union Public Licence (EUPL) v. 1.1, v. 1.2
— Québec Free and Open-Source Licence — Reciprocity (LiLiQ-R) or Strong Reciprocity (LiLiQ-R+). — Québec Free and Open-Source Licence — Reciprocity (LiLiQ-R) or Strong Reciprocity (LiLiQ-R+).
The European Commission may update this Appendix to later versions of the above licences without producing The European Commission may update this Appendix to later versions of the above licences without producing
a new version of the EUPL, as long as they provide the rights granted in Article 2 of this Licence and protect the a new version of the EUPL, as long as they provide the rights granted in Article 2 of this Licence and protect the
covered Source Code from exclusive appropriation. covered Source Code from exclusive appropriation.
All other changes or additions to this Appendix require the production of a new EUPL version. All other changes or additions to this Appendix require the production of a new EUPL version.

34
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@@ -1,17 +1,17 @@
# reactor # reactor
Reactor: Advanced Hydraulic Tank & Biological Process Simulator Reactor: Advanced Hydraulic Tank & Biological Process Simulator
A comprehensive reactor class for wastewater treatment simulation featuring plug flow hydraulics, ASM1-ASM3 biological modeling, and multi-sectional concentration tracking. Implements hydraulic retention time calculations, dispersion modeling, and real-time biological reaction kinetics for accurate process simulation. A comprehensive reactor class for wastewater treatment simulation featuring plug flow hydraulics, ASM1-ASM3 biological modeling, and multi-sectional concentration tracking. Implements hydraulic retention time calculations, dispersion modeling, and real-time biological reaction kinetics for accurate process simulation.
Key Features: Key Features:
Plug Flow Hydraulics: Multi-section reactor with configurable sectioning factor and dispersion modeling Plug Flow Hydraulics: Multi-section reactor with configurable sectioning factor and dispersion modeling
ASM1 Integration: Complete biological nutrient removal modeling with 13 state variables (COD, nitrogen, phosphorus) ASM1 Integration: Complete biological nutrient removal modeling with 13 state variables (COD, nitrogen, phosphorus)
Dynamic Volume Control: Automatic section management with overflow handling and retention time calculations Dynamic Volume Control: Automatic section management with overflow handling and retention time calculations
Oxygen Transfer: Saturation-limited O2 transfer with Fick's law slowdown effects and solubility curves Oxygen Transfer: Saturation-limited O2 transfer with Fick's law slowdown effects and solubility curves
Real-time Kinetics: Continuous biological reaction rate calculations with configurable time acceleration Real-time Kinetics: Continuous biological reaction rate calculations with configurable time acceleration
Weighted Averaging: Volume-based concentration mixing for accurate mass balance calculations Weighted Averaging: Volume-based concentration mixing for accurate mass balance calculations
Child Registration: Integration with diffuser systems and upstream/downstream reactor networks Child Registration: Integration with diffuser systems and upstream/downstream reactor networks
Supports complex biological treatment train modeling with temperature compensation, sludge calculations, and comprehensive process monitoring for wastewater treatment plant optimization and regulatory compliance. Supports complex biological treatment train modeling with temperature compensation, sludge calculations, and comprehensive process monitoring for wastewater treatment plant optimization and regulatory compliance.

114
additional_nodes/recirculation-pump.html
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<script type="text/javascript"> <script type="text/javascript">
RED.nodes.registerType("recirculation-pump", { RED.nodes.registerType("recirculation-pump", {
category: "WWTP", category: "WWTP",
color: "#e4a363", color: "#e4a363",
defaults: { defaults: {
name: { value: "" }, name: { value: "" },
F2: { value: 0, required: true }, F2: { value: 0, required: true },
inlet: { value: 1, required: true } inlet: { value: 1, required: true }
}, },
inputs: 1, inputs: 1,
outputs: 2, outputs: 2,
outputLabels: ["Main effluent", "Recirculation effluent"], outputLabels: ["Main effluent", "Recirculation effluent"],
icon: "font-awesome/fa-random", icon: "font-awesome/fa-random",
label: function() { label: function() {
return this.name || "Recirculation pump"; return this.name || "Recirculation pump";
}, },
oneditprepare: function() { oneditprepare: function() {
$("#node-input-F2").typedInput({ $("#node-input-F2").typedInput({
type:"num", type:"num",
types:["num"] types:["num"]
}); });
$("#node-input-inlet").typedInput({ $("#node-input-inlet").typedInput({
type:"num", type:"num",
types:["num"] types:["num"]
}); });
}, },
oneditsave: function() { oneditsave: function() {
let debit = parseFloat($("#node-input-F2").typedInput("value")); let debit = parseFloat($("#node-input-F2").typedInput("value"));
if (isNaN(debit) || debit < 0) { if (isNaN(debit) || debit < 0) {
RED.notify("Debit is not set correctly", {type: "error"}); RED.notify("Debit is not set correctly", {type: "error"});
} }
let inlet = parseInt($("#node-input-n_inlets").typedInput("value")); let inlet = parseInt($("#node-input-n_inlets").typedInput("value"));
if (inlet < 1) { if (inlet < 1) {
RED.notify("Number of inlets not set correctly", {type: "error"}); RED.notify("Number of inlets not set correctly", {type: "error"});
} }
} }
}); });
</script> </script>
<script type="text/html" data-template-name="recirculation-pump"> <script type="text/html" data-template-name="recirculation-pump">
<div class="form-row"> <div class="form-row">
<label for="node-input-name"><i class="fa fa-tag"></i> Name</label> <label for="node-input-name"><i class="fa fa-tag"></i> Name</label>
<input type="text" id="node-input-name" placeholder="Name"> <input type="text" id="node-input-name" placeholder="Name">
</div> </div>
<div class="form-row"> <div class="form-row">
<label for="node-input-F2"><i class="fa fa-tag"></i> Recirculation debit [m3 d-1]</label> <label for="node-input-F2"><i class="fa fa-tag"></i> Recirculation debit [m3 d-1]</label>
<input type="text" id="node-input-F2" placeholder="m3 s-1"> <input type="text" id="node-input-F2" placeholder="m3 s-1">
</div> </div>
<div class="form-row"> <div class="form-row">
<label for="node-input-inlet"><i class="fa fa-tag"></i> Assigned inlet recirculation</label> <label for="node-input-inlet"><i class="fa fa-tag"></i> Assigned inlet recirculation</label>
<input type="text" id="node-input-inlet" placeholder="#"> <input type="text" id="node-input-inlet" placeholder="#">
</div> </div>
</script> </script>
<script type="text/html" data-help-name="recirculation-pump"> <script type="text/html" data-help-name="recirculation-pump">
<p>Recirculation-pump for splitting streams</p> <p>Recirculation-pump for splitting streams</p>
</script> </script>

80
additional_nodes/recirculation-pump.js
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module.exports = function(RED) { module.exports = function(RED) {
function recirculation(config) { function recirculation(config) {
RED.nodes.createNode(this, config); RED.nodes.createNode(this, config);
var node = this; var node = this;
let name = config.name; let name = config.name;
let F2 = parseFloat(config.F2); let F2 = parseFloat(config.F2);
const inlet_F2 = parseInt(config.inlet); const inlet_F2 = parseInt(config.inlet);
node.on('input', function(msg, send, done) { node.on('input', function(msg, send, done) {
switch (msg.topic) { switch (msg.topic) {
case "Fluent": case "Fluent":
// conserve volume flow debit // conserve volume flow debit
let F_in = msg.payload.F; let F_in = msg.payload.F;
let F1 = Math.max(F_in - F2, 0); let F1 = Math.max(F_in - F2, 0);
let F2_corr = F_in < F2 ? F_in : F2; let F2_corr = F_in < F2 ? F_in : F2;
let msg_F1 = structuredClone(msg); let msg_F1 = structuredClone(msg);
msg_F1.payload.F = F1; msg_F1.payload.F = F1;
let msg_F2 = {...msg}; let msg_F2 = {...msg};
msg_F2.payload.F = F2_corr; msg_F2.payload.F = F2_corr;
msg_F2.payload.inlet = inlet_F2; msg_F2.payload.inlet = inlet_F2;
send([msg_F1, msg_F2]); send([msg_F1, msg_F2]);
break; break;
case "clock": case "clock":
break; break;
default: default:
console.log("Unknown topic: " + msg.topic); console.log("Unknown topic: " + msg.topic);
} }
if (done) { if (done) {
done(); done();
} }
}); });
} }
RED.nodes.registerType("recirculation-pump", recirculation); RED.nodes.registerType("recirculation-pump", recirculation);
}; };

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additional_nodes/settling-basin.html
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<script type="text/javascript"> <script type="text/javascript">
RED.nodes.registerType("settling-basin", { RED.nodes.registerType("settling-basin", {
category: "WWTP", category: "WWTP",
color: "#e4a363", color: "#e4a363",
defaults: { defaults: {
name: { value: "" }, name: { value: "" },
TS_set: { value: 0.1, required: true }, TS_set: { value: 0.1, required: true },
inlet: { value: 1, required: true } inlet: { value: 1, required: true }
}, },
inputs: 1, inputs: 1,
outputs: 2, outputs: 2,
outputLabels: ["Main effluent", "Sludge effluent"], outputLabels: ["Main effluent", "Sludge effluent"],
icon: "font-awesome/fa-random", icon: "font-awesome/fa-random",
label: function() { label: function() {
return this.name || "Settling basin"; return this.name || "Settling basin";
}, },
oneditprepare: function() { oneditprepare: function() {
$("#node-input-TS_set").typedInput({ $("#node-input-TS_set").typedInput({
type:"num", type:"num",
types:["num"] types:["num"]
}); });
$("#node-input-inlet").typedInput({ $("#node-input-inlet").typedInput({
type:"num", type:"num",
types:["num"] types:["num"]
}); });
}, },
oneditsave: function() { oneditsave: function() {
let TS_set = parseFloat($("#node-input-TS_set").typedInput("value")); let TS_set = parseFloat($("#node-input-TS_set").typedInput("value"));
if (isNaN(TS_set) || TS_set < 0) { if (isNaN(TS_set) || TS_set < 0) {
RED.notify("TS is not set correctly", {type: "error"}); RED.notify("TS is not set correctly", {type: "error"});
} }
let inlet = parseInt($("#node-input-n_inlets").typedInput("value")); let inlet = parseInt($("#node-input-n_inlets").typedInput("value"));
if (inlet < 1) { if (inlet < 1) {
RED.notify("Number of inlets not set correctly", {type: "error"}); RED.notify("Number of inlets not set correctly", {type: "error"});
} }
} }
}); });
</script> </script>
<script type="text/html" data-template-name="settling-basin"> <script type="text/html" data-template-name="settling-basin">
<div class="form-row"> <div class="form-row">
<label for="node-input-name"><i class="fa fa-tag"></i> Name</label> <label for="node-input-name"><i class="fa fa-tag"></i> Name</label>
<input type="text" id="node-input-name" placeholder="Name"> <input type="text" id="node-input-name" placeholder="Name">
</div> </div>
<div class="form-row"> <div class="form-row">
<label for="node-input-TS_set"><i class="fa fa-tag"></i> Total Solids set point [g m-3]</label> <label for="node-input-TS_set"><i class="fa fa-tag"></i> Total Solids set point [g m-3]</label>
<input type="text" id="node-input-TS_set" placeholder=""> <input type="text" id="node-input-TS_set" placeholder="">
</div> </div>
<div class="form-row"> <div class="form-row">
<label for="node-input-inlet"><i class="fa fa-tag"></i> Assigned inlet return line</label> <label for="node-input-inlet"><i class="fa fa-tag"></i> Assigned inlet return line</label>
<input type="text" id="node-input-inlet" placeholder="#"> <input type="text" id="node-input-inlet" placeholder="#">
</div> </div>
</script> </script>
<script type="text/html" data-help-name="settling-basin"> <script type="text/html" data-help-name="settling-basin">
<p>Settling tank</p> <p>Settling tank</p>
</script> </script>

114
additional_nodes/settling-basin.js
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module.exports = function(RED) { module.exports = function(RED) {
function settler(config) { function settler(config) {
RED.nodes.createNode(this, config); RED.nodes.createNode(this, config);
var node = this; var node = this;
let name = config.name; let name = config.name;
let TS_set = parseFloat(config.TS_set); let TS_set = parseFloat(config.TS_set);
const inlet_sludge = parseInt(config.inlet); const inlet_sludge = parseInt(config.inlet);
node.on('input', function(msg, send, done) { node.on('input', function(msg, send, done) {
switch (msg.topic) { switch (msg.topic) {
case "Fluent": case "Fluent":
// conserve volume flow debit // conserve volume flow debit
let F_in = msg.payload.F; let F_in = msg.payload.F;
let C_in = msg.payload.C; let C_in = msg.payload.C;
let F2 = (F_in * C_in[12]) / TS_set; let F2 = (F_in * C_in[12]) / TS_set;
let F1 = Math.max(F_in - F2, 0); let F1 = Math.max(F_in - F2, 0);
let F2_corr = F_in < F2 ? F_in : F2; let F2_corr = F_in < F2 ? F_in : F2;
let msg_F1 = structuredClone(msg); let msg_F1 = structuredClone(msg);
msg_F1.payload.F = F1; msg_F1.payload.F = F1;
msg_F1.payload.C[7] = 0; msg_F1.payload.C[7] = 0;
msg_F1.payload.C[8] = 0; msg_F1.payload.C[8] = 0;
msg_F1.payload.C[9] = 0; msg_F1.payload.C[9] = 0;
msg_F1.payload.C[10] = 0; msg_F1.payload.C[10] = 0;
msg_F1.payload.C[11] = 0; msg_F1.payload.C[11] = 0;
msg_F1.payload.C[12] = 0; msg_F1.payload.C[12] = 0;
let msg_F2 = {...msg}; let msg_F2 = {...msg};
msg_F2.payload.F = F2_corr; msg_F2.payload.F = F2_corr;
if (F2_corr > 0) { if (F2_corr > 0) {
msg_F2.payload.C[7] = F_in * C_in[7] / F2; msg_F2.payload.C[7] = F_in * C_in[7] / F2;
msg_F2.payload.C[8] = F_in * C_in[8] / F2; msg_F2.payload.C[8] = F_in * C_in[8] / F2;
msg_F2.payload.C[9] = F_in * C_in[9] / F2; msg_F2.payload.C[9] = F_in * C_in[9] / F2;
msg_F2.payload.C[10] = F_in * C_in[10] / F2; msg_F2.payload.C[10] = F_in * C_in[10] / F2;
msg_F2.payload.C[11] = F_in * C_in[11] / F2; msg_F2.payload.C[11] = F_in * C_in[11] / F2;
msg_F2.payload.C[12] = F_in * C_in[12] / F2; msg_F2.payload.C[12] = F_in * C_in[12] / F2;
} }
msg_F2.payload.inlet = inlet_sludge; msg_F2.payload.inlet = inlet_sludge;
send([msg_F1, msg_F2]); send([msg_F1, msg_F2]);
break; break;
case "clock": case "clock":
break; break;
default: default:
console.log("Unknown topic: " + msg.topic); console.log("Unknown topic: " + msg.topic);
} }
if (done) { if (done) {
done(); done();
} }
}); });
} }
RED.nodes.registerType("settling-basin", settler); RED.nodes.registerType("settling-basin", settler);
}; };

8
examples/README.md
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@@ -1,8 +0,0 @@
# reactor Example Flows
Import-ready Node-RED examples for reactor.
## Files
- basic.flow.json
- integration.flow.json
- edge.flow.json

6
examples/basic.flow.json
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[
{"id":"reactor_basic_tab","type":"tab","label":"reactor basic","disabled":false,"info":"reactor basic example"},
{"id":"reactor_basic_node","type":"reactor","z":"reactor_basic_tab","name":"reactor basic","x":420,"y":180,"wires":[["reactor_basic_dbg"]]},
{"id":"reactor_basic_inj","type":"inject","z":"reactor_basic_tab","name":"basic trigger","props":[{"p":"topic","vt":"str"},{"p":"payload","vt":"str"}],"topic":"ping","payload":"1","payloadType":"str","x":160,"y":180,"wires":[["reactor_basic_node"]]},
{"id":"reactor_basic_dbg","type":"debug","z":"reactor_basic_tab","name":"reactor basic debug","active":true,"tosidebar":true,"console":false,"tostatus":false,"complete":"true","targetType":"full","x":660,"y":180,"wires":[]}
]

6
examples/edge.flow.json
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[
{"id":"reactor_edge_tab","type":"tab","label":"reactor edge","disabled":false,"info":"reactor edge example"},
{"id":"reactor_edge_node","type":"reactor","z":"reactor_edge_tab","name":"reactor edge","x":420,"y":180,"wires":[["reactor_edge_dbg"]]},
{"id":"reactor_edge_inj","type":"inject","z":"reactor_edge_tab","name":"unknown topic","props":[{"p":"topic","vt":"str"},{"p":"payload","vt":"str"}],"topic":"doesNotExist","payload":"x","payloadType":"str","x":170,"y":180,"wires":[["reactor_edge_node"]]},
{"id":"reactor_edge_dbg","type":"debug","z":"reactor_edge_tab","name":"reactor edge debug","active":true,"tosidebar":true,"console":false,"tostatus":false,"complete":"true","targetType":"full","x":660,"y":180,"wires":[]}
]

6
examples/integration.flow.json
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@@ -1,6 +0,0 @@
[
{"id":"reactor_int_tab","type":"tab","label":"reactor integration","disabled":false,"info":"reactor integration example"},
{"id":"reactor_int_node","type":"reactor","z":"reactor_int_tab","name":"reactor integration","x":420,"y":180,"wires":[["reactor_int_dbg"]]},
{"id":"reactor_int_inj","type":"inject","z":"reactor_int_tab","name":"registerChild","props":[{"p":"topic","vt":"str"},{"p":"payload","vt":"str"}],"topic":"registerChild","payload":"example-child-id","payloadType":"str","x":170,"y":180,"wires":[["reactor_int_node"]]},
{"id":"reactor_int_dbg","type":"debug","z":"reactor_int_tab","name":"reactor integration debug","active":true,"tosidebar":true,"console":false,"tostatus":false,"complete":"true","targetType":"full","x":680,"y":180,"wires":[]}
]

3524
flows/asm3_flows.json
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238
package-lock.json generated
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@@ -1,119 +1,119 @@
{ {
"name": "reactor", "name": "reactor",
"version": "0.0.1", "version": "0.0.1",
"lockfileVersion": 3, "lockfileVersion": 3,
"requires": true, "requires": true,
"packages": { "packages": {
"": { "": {
"name": "reactor", "name": "reactor",
"version": "0.0.1", "version": "0.0.1",
"license": "SEE LICENSE", "license": "SEE LICENSE",
"dependencies": { "dependencies": {
"generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/RnD/generalFunctions.git", "generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/RnD/generalFunctions.git",
"mathjs": "^14.5.2" "mathjs": "^14.5.2"
} }
}, },
"node_modules/@babel/runtime": { "node_modules/@babel/runtime": {
"version": "7.28.4", "version": "7.28.4",
"resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.28.4.tgz", "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.28.4.tgz",
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"engines": { "engines": {
"node": "*" "node": "*"
}, },
"funding": { "funding": {
"type": "github", "type": "github",
"url": "https://github.com/sponsors/rawify" "url": "https://github.com/sponsors/rawify"
} }
}, },
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"license": "MIT" "license": "MIT"
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"node_modules/fraction.js": { "node_modules/fraction.js": {
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"engines": { "engines": {
"node": "*" "node": "*"
}, },
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"type": "github", "type": "github",
"url": "https://github.com/sponsors/rawify" "url": "https://github.com/sponsors/rawify"
} }
}, },
"node_modules/generalFunctions": { "node_modules/generalFunctions": {
"version": "1.0.0", "version": "1.0.0",
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"license": "SEE LICENSE" "license": "SEE LICENSE"
}, },
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"license": "MIT" "license": "MIT"
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64
package.json
View File

@@ -1,33 +1,33 @@
{ {
"name": "reactor", "name": "reactor",
"version": "0.0.1", "version": "0.0.1",
"description": "Implementation of the asm3 model for Node-Red", "description": "Implementation of the asm3 model for Node-Red",
"repository": { "repository": {
"type": "git", "type": "git",
"url": "https://gitea.centraal.wbd-rd.nl/RnD/reactor.git" "url": "https://gitea.centraal.wbd-rd.nl/RnD/reactor.git"
},
"keywords": [
"asm3",
"activated sludge",
"wastewater",
"biological model",
"node-red"
],
"license": "SEE LICENSE",
"author": "P.R. van der Wilt",
"main": "reactor.js",
"scripts": {
"test": "node --test test/basic/*.test.js test/integration/*.test.js test/edge/*.test.js"
}, },
"node-red": { "keywords": [
"nodes": { "asm3",
"reactor": "reactor.js", "activated sludge",
"recirculation-pump": "additional_nodes/recirculation-pump.js", "wastewater",
"settling-basin": "additional_nodes/settling-basin.js" "biological model",
} "node-red"
}, ],
"dependencies": { "license": "SEE LICENSE",
"generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/RnD/generalFunctions.git", "author": "P.R. van der Wilt",
"mathjs": "^14.5.2" "main": "reactor.js",
} "scripts": {
} "test": "node reactor.js"
},
"node-red": {
"nodes": {
"reactor": "reactor.js",
"recirculation-pump": "additional_nodes/recirculation-pump.js",
"settling-basin": "additional_nodes/settling-basin.js"
}
},
"dependencies": {
"generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/RnD/generalFunctions.git",
"mathjs": "^14.5.2"
}
}

515
reactor.html
View File

@@ -1,267 +1,248 @@
<!-- <script src="/reactor/menu.js"></script>
| S88-niveau | Primair (blokkleur) | Tekstkleur |
| ---------------------- | ------------------- | ---------- | <script type="text/javascript">
| **Area** | `#0f52a5` | wit | RED.nodes.registerType("reactor", {
| **Process Cell** | `#0c99d9` | wit | category: "WWTP",
| **Unit** | `#50a8d9` | zwart | color: "#c4cce0",
| **Equipment (Module)** | `#86bbdd` | zwart | defaults: {
| **Control Module** | `#a9daee` | zwart | name: { value: "" },
reactor_type: { value: "CSTR", required: true },
--> volume: { value: 0., required: true },
<script src="/reactor/menu.js"></script> length: { value: 0.},
resolution_L: { value: 0.},
<script type="text/javascript"> alpha: {value: 0},
RED.nodes.registerType("reactor", { n_inlets: { value: 1, required: true},
category: "EVOLV", kla: { value: null },
color: "#50a8d9",
defaults: { S_O_init: { value: 0., required: true },
name: { value: "" }, S_I_init: { value: 30., required: true },
reactor_type: { value: "CSTR", required: true }, S_S_init: { value: 100., required: true },
volume: { value: 0., required: true }, S_NH_init: { value: 16., required: true },
length: { value: 0.}, S_N2_init: { value: 0., required: true },
resolution_L: { value: 0.}, S_NO_init: { value: 0., required: true },
alpha: {value: 0}, S_HCO_init: { value: 5., required: true },
n_inlets: { value: 1, required: true}, X_I_init: { value: 25., required: true },
kla: { value: null }, X_S_init: { value: 75., required: true },
X_H_init: { value: 30., required: true },
S_O_init: { value: 0., required: true }, X_STO_init: { value: 0., required: true },
S_I_init: { value: 30., required: true }, X_A_init: { value: 0.001, required: true },
S_S_init: { value: 100., required: true }, X_TS_init: { value: 125.0009, required: true },
S_NH_init: { value: 16., required: true },
S_N2_init: { value: 0., required: true }, timeStep: { value: 1, required: true },
S_NO_init: { value: 0., required: true },
S_HCO_init: { value: 5., required: true }, enableLog: { value: false },
X_I_init: { value: 25., required: true }, logLevel: { value: "error" },
X_S_init: { value: 75., required: true },
X_H_init: { value: 30., required: true }, positionVsParent: { value: "" },
X_STO_init: { value: 0., required: true }, },
X_A_init: { value: 0.001, required: true }, inputs: 1,
X_TS_init: { value: 125.0009, required: true }, outputs: 3,
inputLabels: ["input"],
timeStep: { value: 1, required: true }, outputLabels: ["process", "dbase", "parent"],
speedUpFactor: { value: 1 }, icon: "font-awesome/fa-recycle",
label: function() {
enableLog: { value: false }, return this.name || "Reactor";
logLevel: { value: "error" }, },
oneditprepare: function() {
positionVsParent: { value: "" }, // wait for the menu scripts to load
}, const waitForMenuData = () => {
inputs: 1, if (window.EVOLV?.nodes?.reactor?.initEditor) {
outputs: 3, window.EVOLV.nodes.reactor.initEditor(this);
inputLabels: ["input"], } else {
outputLabels: ["process", "dbase", "parent"], setTimeout(waitForMenuData, 50);
icon: "font-awesome/fa-flask", }
label: function() { };
return this.name || "Reactor"; waitForMenuData();
},
oneditprepare: function() { $("#node-input-volume").typedInput({
// wait for the menu scripts to load type:"num",
const waitForMenuData = () => { types:["num"]
if (window.EVOLV?.nodes?.reactor?.initEditor) { });
window.EVOLV.nodes.reactor.initEditor(this); $("#node-input-n_inlets").typedInput({
} else { type:"num",
setTimeout(waitForMenuData, 50); types:["num"]
} });
}; $("#node-input-length").typedInput({
waitForMenuData(); type:"num",
types:["num"]
$("#node-input-volume").typedInput({ });
type:"num", $("#node-input-resolution_L").typedInput({
types:["num"] type:"num",
}); types:["num"]
$("#node-input-n_inlets").typedInput({ });
type:"num", $("#node-input-kla").typedInput({
types:["num"] type:"num",
}); types:["num"]
$("#node-input-length").typedInput({ });
type:"num", $(".concentrations").typedInput({
types:["num"] type:"num",
}); types:["num"]
$("#node-input-resolution_L").typedInput({ });
type:"num", $("#node-input-reactor_type").typedInput({
types:["num"] types: [
}); {
$("#node-input-kla").typedInput({ value: "CSTR",
type:"num", options: [
types:["num"] { value: "CSTR", label: "CSTR"},
}); { value: "PFR", label: "PFR"}
$(".concentrations").typedInput({ ]
type:"num", }
types:["num"] ]
}); })
$("#node-input-reactor_type").typedInput({ $("#node-input-reactor_type").on("change", function() {
types: [ const type = $("#node-input-reactor_type").typedInput("value");
{ if (type === "CSTR") {
value: "CSTR", $(".PFR").hide();
options: [ } else {
{ value: "CSTR", label: "CSTR"}, $(".PFR").show();
{ value: "PFR", label: "PFR"} }
] });
} $("#node-input-alpha").typedInput({
] type:"num",
}) types:["num"]
$("#node-input-reactor_type").on("change", function() { })
const type = $("#node-input-reactor_type").typedInput("value"); $("#node-input-timeStep").typedInput({
if (type === "CSTR") { type:"num",
$(".PFR").hide(); types:["num"]
} else { })
$(".PFR").show(); // Set initial visibility on dialog open
} const initialType = $("#node-input-reactor_type").typedInput("value");
}); if (initialType === "CSTR") {
$("#node-input-alpha").typedInput({ $(".PFR").hide();
type:"num", } else {
types:["num"] $(".PFR").show();
}) }
$("#node-input-timeStep").typedInput({ },
type:"num", oneditsave: function() {
types:["num"] // save logger fields
}) if (window.EVOLV?.nodes?.reactor?.loggerMenu?.saveEditor) {
$("#node-input-speedUpFactor").typedInput({ window.EVOLV.nodes.reactor.loggerMenu.saveEditor(this);
type:"num", }
types:["num"]
}) // save position field
// Set initial visibility on dialog open if (window.EVOLV?.nodes?.measurement?.positionMenu?.saveEditor) {
const initialType = $("#node-input-reactor_type").typedInput("value"); window.EVOLV.nodes.rotatingMachine.positionMenu.saveEditor(this);
if (initialType === "CSTR") { }
$(".PFR").hide();
} else { let volume = parseFloat($("#node-input-volume").typedInput("value"));
$(".PFR").show(); if (isNaN(volume) || volume <= 0) {
} RED.notify("Fluid volume not set correctly", {type: "error"});
}, }
oneditsave: function() { let n_inlets = parseInt($("#node-input-n_inlets").typedInput("value"));
// save logger fields if (isNaN(n_inlets) || n_inlets < 1) {
if (window.EVOLV?.nodes?.reactor?.loggerMenu?.saveEditor) { RED.notify("Number of inlets not set correctly", {type: "error"});
window.EVOLV.nodes.reactor.loggerMenu.saveEditor(this); }
} }
});
// save position field </script>
if (window.EVOLV?.nodes?.reactor?.positionMenu?.saveEditor) {
window.EVOLV.nodes.reactor.positionMenu.saveEditor(this); <script type="text/html" data-template-name="reactor">
} <div class="form-row">
<label for="node-input-name"><i class="fa fa-tag"></i> Name</label>
let volume = parseFloat($("#node-input-volume").typedInput("value")); <input type="text" id="node-input-name" placeholder="Name">
if (isNaN(volume) || volume <= 0) { </div>
RED.notify("Fluid volume not set correctly", {type: "error"}); <h2> Reactor properties </h2>
} <div class="form-row">
let n_inlets = parseInt($("#node-input-n_inlets").typedInput("value")); <label for="node-input-reactor_type"><i class="fa fa-tag"></i> Reactor type</label>
if (isNaN(n_inlets) || n_inlets < 1) { <input type="text" id="node-input-reactor_type">
RED.notify("Number of inlets not set correctly", {type: "error"}); </div>
} <div class="form-row">
} <label for="node-input-volume"><i class="fa fa-tag"></i> Fluid volume [m3]</label>
}); <input type="text" id="node-input-volume" placeholder="m3">
</script> </div>
<div class="form-row PFR">
<script type="text/html" data-template-name="reactor"> <label for="node-input-length"><i class="fa fa-tag"></i> Reactor length [m]</label>
<div class="form-row"> <input type="text" id="node-input-length" placeholder="m">
<label for="node-input-name"><i class="fa fa-tag"></i> Name</label> </div>
<input type="text" id="node-input-name" placeholder="Name"> <div class="form-row PFR">
</div> <label for="node-input-resolution_L"><i class="fa fa-tag"></i> Resolution</label>
<h2> Reactor properties </h2> <input type="text" id="node-input-resolution_L" placeholder="#">
<div class="form-row"> </div>
<label for="node-input-reactor_type"><i class="fa fa-tag"></i> Reactor type</label> <div class="PFR">
<input type="text" id="node-input-reactor_type"> <p> Inlet boundary condition parameter &alpha; (&alpha; = 0: Danckwerts BC / &alpha; = 1: Dirichlet BC) </p>
</div> <div class="form-row">
<div class="form-row"> <label for="node-input-alpha"><i class="fa fa-tag"></i>Adjustable parameter BC</label>
<label for="node-input-volume"><i class="fa fa-tag"></i> Fluid volume [m3]</label> <input type="text" id="node-input-alpha">
<input type="text" id="node-input-volume" placeholder="m3"> </div>
</div> </div>
<div class="form-row PFR"> <div class="form-row">
<label for="node-input-length"><i class="fa fa-tag"></i> Reactor length [m]</label> <label for="node-input-n_inlets"><i class="fa fa-tag"></i> Number of inlets</label>
<input type="text" id="node-input-length" placeholder="m"> <input type="text" id="node-input-n_inlets" placeholder="#">
</div> </div>
<div class="form-row PFR"> <h3> Internal mass transfer calculation (optional) </h3>
<label for="node-input-resolution_L"><i class="fa fa-tag"></i> Resolution</label> <div class="form-row">
<input type="text" id="node-input-resolution_L" placeholder="#"> <label for="node-input-kla"><i class="fa fa-tag"></i> kLa [d-1]</label>
</div> <input type="text" id="node-input-kla" placeholder="d-1">
<div class="PFR"> </div>
<p> Inlet boundary condition parameter &alpha; (&alpha; = 0: Danckwerts BC / &alpha; = 1: Dirichlet BC) </p> <h2> Dissolved components </h2>
<div class="form-row"> <div class="form-row">
<label for="node-input-alpha"><i class="fa fa-tag"></i>Adjustable parameter BC</label> <label for="node-input-S_O_init"><i class="fa fa-tag"></i> Initial dissolved oxygen [g O2 m-3]</label>
<input type="text" id="node-input-alpha"> <input type="text" id="node-input-S_O_init" class="concentrations">
</div> </div>
</div> <div class="form-row">
<div class="form-row"> <label for="node-input-S_I_init"><i class="fa fa-tag"></i> Initial soluble inert organics [g COD m-3]</label>
<label for="node-input-n_inlets"><i class="fa fa-tag"></i> Number of inlets</label> <input type="text" id="node-input-S_I_init" class="concentrations">
<input type="text" id="node-input-n_inlets" placeholder="#"> </div>
</div> <div class="form-row">
<h3> Internal mass transfer calculation (optional) </h3> <label for="node-input-S_S_init"><i class="fa fa-tag"></i> Initial readily biodegrable substrates [g COD m-3]</label>
<div class="form-row"> <input type="text" id="node-input-S_S_init" class="concentrations">
<label for="node-input-kla"><i class="fa fa-tag"></i> kLa [d-1]</label> </div>
<input type="text" id="node-input-kla" placeholder="d-1"> <div class="form-row">
</div> <label for="node-input-S_NH_init"><i class="fa fa-tag"></i> Initial ammonium / ammonia [g N m-3]</label>
<h2> Dissolved components </h2> <input type="text" id="node-input-S_NH_init" class="concentrations">
<div class="form-row"> </div>
<label for="node-input-S_O_init"><i class="fa fa-tag"></i> Initial dissolved oxygen [g O2 m-3]</label> <div class="form-row">
<input type="text" id="node-input-S_O_init" class="concentrations"> <label for="node-input-S_N2_init"><i class="fa fa-tag"></i> Initial dinitrogen, released by denitrification [g N m-3]</label>
</div> <input type="text" id="node-input-S_N2_init" class="concentrations">
<div class="form-row"> </div>
<label for="node-input-S_I_init"><i class="fa fa-tag"></i> Initial soluble inert organics [g COD m-3]</label> <div class="form-row">
<input type="text" id="node-input-S_I_init" class="concentrations"> <label for="node-input-S_NO_init"><i class="fa fa-tag"></i> Initial nitrite + nitrate [g N m-3]</label>
</div> <input type="text" id="node-input-S_NO_init" class="concentrations">
<div class="form-row"> </div>
<label for="node-input-S_S_init"><i class="fa fa-tag"></i> Initial readily biodegrable substrates [g COD m-3]</label> <div class="form-row">
<input type="text" id="node-input-S_S_init" class="concentrations"> <label for="node-input-S_HCO_init"><i class="fa fa-tag"></i> Initial alkalinity, bicarbonate [mole HCO3- m-3]</label>
</div> <input type="text" id="node-input-S_HCO_init" class="concentrations">
<div class="form-row"> </div>
<label for="node-input-S_NH_init"><i class="fa fa-tag"></i> Initial ammonium / ammonia [g N m-3]</label> <h2> Particulate components </h2>
<input type="text" id="node-input-S_NH_init" class="concentrations"> <div class="form-row">
</div> <label for="node-input-X_I_init"><i class="fa fa-tag"></i> Initial inert particulate organics [g COD m-3]</label>
<div class="form-row"> <input type="text" id="node-input-X_I_init" class="concentrations">
<label for="node-input-S_N2_init"><i class="fa fa-tag"></i> Initial dinitrogen, released by denitrification [g N m-3]</label> </div>
<input type="text" id="node-input-S_N2_init" class="concentrations"> <div class="form-row">
</div> <label for="node-input-X_S_init"><i class="fa fa-tag"></i> Initial slowly biodegrable substrates [g COD m-3]</label>
<div class="form-row"> <input type="text" id="node-input-X_S_init" class="concentrations">
<label for="node-input-S_NO_init"><i class="fa fa-tag"></i> Initial nitrite + nitrate [g N m-3]</label> </div>
<input type="text" id="node-input-S_NO_init" class="concentrations"> <div class="form-row">
</div> <label for="node-input-X_H_init"><i class="fa fa-tag"></i> Initial heterotrophic biomass [g COD m-3]</label>
<div class="form-row"> <input type="text" id="node-input-X_H_init" class="concentrations">
<label for="node-input-S_HCO_init"><i class="fa fa-tag"></i> Initial alkalinity, bicarbonate [mole HCO3- m-3]</label> </div>
<input type="text" id="node-input-S_HCO_init" class="concentrations"> <div class="form-row">
</div> <label for="node-input-X_STO_init"><i class="fa fa-tag"></i> Initial Organics stored by heterotrophs [g COD m-3]</label>
<h2> Particulate components </h2> <input type="text" id="node-input-X_STO_init" class="concentrations">
<div class="form-row"> </div>
<label for="node-input-X_I_init"><i class="fa fa-tag"></i> Initial inert particulate organics [g COD m-3]</label> <div class="form-row">
<input type="text" id="node-input-X_I_init" class="concentrations"> <label for="node-input-X_A_init"><i class="fa fa-tag"></i> Initial autotrophic, nitrifying biomass [g COD m-3]</label>
</div> <input type="text" id="node-input-X_A_init" class="concentrations">
<div class="form-row"> </div>
<label for="node-input-X_S_init"><i class="fa fa-tag"></i> Initial slowly biodegrable substrates [g COD m-3]</label> <div class="form-row">
<input type="text" id="node-input-X_S_init" class="concentrations"> <label for="node-input-X_TS_init"><i class="fa fa-tag"></i> Initial total suspended solids [g TSS m-3]</label>
</div> <input type="text" id="node-input-X_TS_init" class="concentrations">
<div class="form-row"> </div>
<label for="node-input-X_H_init"><i class="fa fa-tag"></i> Initial heterotrophic biomass [g COD m-3]</label> <h2> Simulation parameters </h2>
<input type="text" id="node-input-X_H_init" class="concentrations"> <div class="form-row">
</div> <label for="node-input-timeStep"><i class="fa fa-tag"></i> Time step [s]</label>
<div class="form-row"> <input type="text" id="node-input-timeStep" placeholder="s">
<label for="node-input-X_STO_init"><i class="fa fa-tag"></i> Initial Organics stored by heterotrophs [g COD m-3]</label> </div>
<input type="text" id="node-input-X_STO_init" class="concentrations">
</div> <!-- Logger fields injected here -->
<div class="form-row"> <div id="logger-fields-placeholder"></div>
<label for="node-input-X_A_init"><i class="fa fa-tag"></i> Initial autotrophic, nitrifying biomass [g COD m-3]</label>
<input type="text" id="node-input-X_A_init" class="concentrations"> <!-- Position fields will be injected here -->
</div> <div id="position-fields-placeholder"></div>
<div class="form-row">
<label for="node-input-X_TS_init"><i class="fa fa-tag"></i> Initial total suspended solids [g TSS m-3]</label>
<input type="text" id="node-input-X_TS_init" class="concentrations"> </script>
</div>
<h2> Simulation parameters </h2> <script type="text/html" data-help-name="reactor">
<div class="form-row"> <p>New reactor node</p>
<label for="node-input-timeStep"><i class="fa fa-tag"></i> Time step [s]</label> </script>
<input type="text" id="node-input-timeStep" placeholder="s">
</div>
<div class="form-row">
<label for="node-input-speedUpFactor"><i class="fa fa-tag"></i> Speed-up factor</label>
<input type="text" id="node-input-speedUpFactor" placeholder="1 = real-time">
</div>
<!-- Logger fields injected here -->
<div id="logger-fields-placeholder"></div>
<!-- Position fields will be injected here -->
<div id="position-fields-placeholder"></div>
</script>
<script type="text/html" data-help-name="reactor">
<p>New reactor node</p>
</script>

52
reactor.js
View File

@@ -1,26 +1,26 @@
const nameOfNode = "reactor"; // name of the node, should match file name and node type in Node-RED const nameOfNode = "reactor"; // name of the node, should match file name and node type in Node-RED
const nodeClass = require('./src/nodeClass.js'); // node class const nodeClass = require('./src/nodeClass.js'); // node class
const { MenuManager } = require('generalFunctions'); const { MenuManager } = require('generalFunctions');
module.exports = function (RED) { module.exports = function (RED) {
// Register the node type // Register the node type
RED.nodes.registerType(nameOfNode, function (config) { RED.nodes.registerType(nameOfNode, function (config) {
// Initialize the Node-RED node first // Initialize the Node-RED node first
RED.nodes.createNode(this, config); RED.nodes.createNode(this, config);
// Then create your custom class and attach it // Then create your custom class and attach it
this.nodeClass = new nodeClass(config, RED, this, nameOfNode); this.nodeClass = new nodeClass(config, RED, this, nameOfNode);
}); });
const menuMgr = new MenuManager(); const menuMgr = new MenuManager();
// Serve /advancedReactor/menu.js // Serve /advancedReactor/menu.js
RED.httpAdmin.get(`/${nameOfNode}/menu.js`, (req, res) => { RED.httpAdmin.get(`/${nameOfNode}/menu.js`, (req, res) => {
try { try {
const script = menuMgr.createEndpoint(nameOfNode, ['logger', 'position']); const script = menuMgr.createEndpoint(nameOfNode, ['logger', 'position']);
res.type('application/javascript').send(script); res.type('application/javascript').send(script);
} catch (err) { } catch (err) {
res.status(500).send(`// Error generating menu: ${err.message}`); res.status(500).send(`// Error generating menu: ${err.message}`);
} }
}); });
}; };

347
src/nodeClass.js
View File

@@ -1,218 +1,165 @@
const { Reactor_CSTR, Reactor_PFR } = require('./specificClass.js'); const { Reactor_CSTR, Reactor_PFR } = require('./specificClass.js');
const { outputUtils } = require('generalFunctions');
const REACTOR_SPECIES = [
'S_O', class nodeClass {
'S_I', /**
'S_S', * Node-RED node class for advanced-reactor.
'S_NH', * @param {object} uiConfig - Node-RED node configuration
'S_N2', * @param {object} RED - Node-RED runtime API
'S_NO', * @param {object} nodeInstance - Node-RED node instance
'S_HCO', * @param {string} nameOfNode - Name of the node
'X_I', */
'X_S', constructor(uiConfig, RED, nodeInstance, nameOfNode) {
'X_H', // Preserve RED reference for HTTP endpoints if needed
'X_STO', this.node = nodeInstance;
'X_A', this.RED = RED;
'X_TS' this.name = nameOfNode;
]; this.source = null;
class nodeClass {
/**
* Node-RED node class for advanced-reactor.
* @param {object} uiConfig - Node-RED node configuration
* @param {object} RED - Node-RED runtime API
* @param {object} nodeInstance - Node-RED node instance
* @param {string} nameOfNode - Name of the node
*/
constructor(uiConfig, RED, nodeInstance, nameOfNode) {
// Preserve RED reference for HTTP endpoints if needed
this.node = nodeInstance;
this.RED = RED;
this.name = nameOfNode;
this.source = null;
this._loadConfig(uiConfig) this._loadConfig(uiConfig)
this._setupClass(); this._setupClass();
this._output = new outputUtils();
this._attachInputHandler(); this._attachInputHandler();
this._registerChild(); this._registerChild();
this._startTickLoop(); this._startTickLoop();
this._attachCloseHandler(); this._attachCloseHandler();
}
/**
* Handle node-red input messages
*/
_attachInputHandler() {
this.node.on('input', (msg, send, done) => {
try {
switch (msg.topic) {
case "clock":
this.source.updateState(msg.timestamp);
send([msg, null, null]);
break;
case "Fluent":
this.source.setInfluent = msg;
break;
case "OTR":
this.source.setOTR = msg;
break;
case "Temperature":
this.source.setTemperature = msg;
break;
case "Dispersion":
this.source.setDispersion = msg;
break;
case 'registerChild': {
const childId = msg.payload;
const childObj = this.RED.nodes.getNode(childId);
if (!childObj || !childObj.source) {
this.source?.logger?.warn(`registerChild skipped: missing child/source for id=${childId}`);
break;
}
this.source.childRegistrationUtils.registerChild(childObj.source, msg.positionVsParent);
break;
}
default:
this.source?.logger?.warn(`Unknown topic: ${msg.topic}`);
}
} catch (error) {
this.source?.logger?.error(`Input handler failure: ${error.message}`);
}
if (typeof done === 'function') {
done();
}
});
}
/**
* Parse node configuration
* @param {object} uiConfig Config set in UI in node-red
*/
_loadConfig(uiConfig) {
this.config = {
general: {
name: uiConfig.name || this.name,
id: this.node.id,
unit: null,
logging: {
enabled: uiConfig.enableLog,
logLevel: uiConfig.logLevel
}
},
functionality: {
positionVsParent: uiConfig.positionVsParent || 'atEquipment', // Default to 'atEquipment' if not specified
softwareType: "reactor" // should be set in config manager
},
reactor_type: uiConfig.reactor_type,
volume: parseFloat(uiConfig.volume),
length: parseFloat(uiConfig.length),
resolution_L: parseInt(uiConfig.resolution_L),
alpha: parseFloat(uiConfig.alpha),
n_inlets: parseInt(uiConfig.n_inlets),
kla: parseFloat(uiConfig.kla),
initialState: [
parseFloat(uiConfig.S_O_init),
parseFloat(uiConfig.S_I_init),
parseFloat(uiConfig.S_S_init),
parseFloat(uiConfig.S_NH_init),
parseFloat(uiConfig.S_N2_init),
parseFloat(uiConfig.S_NO_init),
parseFloat(uiConfig.S_HCO_init),
parseFloat(uiConfig.X_I_init),
parseFloat(uiConfig.X_S_init),
parseFloat(uiConfig.X_H_init),
parseFloat(uiConfig.X_STO_init),
parseFloat(uiConfig.X_A_init),
parseFloat(uiConfig.X_TS_init)
],
timeStep: parseFloat(uiConfig.timeStep),
speedUpFactor: Number(uiConfig.speedUpFactor) || 1
}
}
/**
* Register this node as a child upstream and downstream.
* Delayed to avoid Node-RED startup race conditions.
*/
_registerChild() {
setTimeout(() => {
this.node.send([
null,
null,
{ topic: 'registerChild', payload: this.node.id, positionVsParent: this.config?.functionality?.positionVsParent || 'atEquipment' }
]);
}, 100);
}
/**
* Setup reactor class based on config
*/
_setupClass() {
let new_reactor;
switch (this.config.reactor_type) {
case "CSTR":
new_reactor = new Reactor_CSTR(this.config);
break;
case "PFR":
new_reactor = new Reactor_PFR(this.config);
break;
default:
this.node.warn("Unknown reactor type: " + this.config.reactor_type + ". Falling back to CSTR.");
new_reactor = new Reactor_CSTR(this.config);
}
this.source = new_reactor; // protect from reassignment
this.node.source = this.source;
}
_startTickLoop() {
setTimeout(() => {
this._tickInterval = setInterval(() => this._tick(), 1000);
}, 1000);
}
_tick(){
const gridProfile = this.source.getGridProfile;
if (gridProfile) {
this.node.send([{ topic: "GridProfile", payload: gridProfile }, null, null]);
}
this.node.send([this.source.getEffluent, this._buildTelemetryMessage(), null]);
} }
_buildTelemetryMessage() { /**
const effluent = this.source?.getEffluent; * Handle node-red input messages
const concentrations = effluent?.payload?.C; */
if (!Array.isArray(concentrations)) { _attachInputHandler() {
return null; this.node.on('input', (msg, send, done) => {
}
const telemetry = { switch (msg.topic) {
flow_total: Number(effluent.payload.F), case "clock":
temperature: Number(this.source?.temperature), this.source.updateState(msg.timestamp);
}; send([msg, null, null]);
break;
for (let i = 0; i < Math.min(REACTOR_SPECIES.length, concentrations.length); i += 1) { case "Fluent":
const value = Number(concentrations[i]); this.source.setInfluent = msg;
if (Number.isFinite(value)) { break;
telemetry[REACTOR_SPECIES[i]] = value; case "OTR":
this.source.setOTR = msg;
break;
case "Temperature":
this.source.setTemperature = msg;
break;
case "Dispersion":
this.source.setDispersion = msg;
break;
case 'registerChild':
// Register this node as a parent of the child node
const childId = msg.payload;
const childObj = this.RED.nodes.getNode(childId);
this.source.childRegistrationUtils.registerChild(childObj.source, msg.positionVsParent);
break;
default:
console.log("Unknown topic: " + msg.topic);
} }
if (done) {
done();
}
});
}
/**
* Parse node configuration
* @param {object} uiConfig Config set in UI in node-red
*/
_loadConfig(uiConfig) {
this.config = {
general: {
name: uiConfig.name || this.name,
id: this.node.id,
unit: null,
logging: {
enabled: uiConfig.enableLog,
logLevel: uiConfig.logLevel
}
},
functionality: {
positionVsParent: uiConfig.positionVsParent || 'atEquipment', // Default to 'atEquipment' if not specified
softwareType: "reactor" // should be set in config manager
},
reactor_type: uiConfig.reactor_type,
volume: parseFloat(uiConfig.volume),
length: parseFloat(uiConfig.length),
resolution_L: parseInt(uiConfig.resolution_L),
alpha: parseFloat(uiConfig.alpha),
n_inlets: parseInt(uiConfig.n_inlets),
kla: parseFloat(uiConfig.kla),
initialState: [
parseFloat(uiConfig.S_O_init),
parseFloat(uiConfig.S_I_init),
parseFloat(uiConfig.S_S_init),
parseFloat(uiConfig.S_NH_init),
parseFloat(uiConfig.S_N2_init),
parseFloat(uiConfig.S_NO_init),
parseFloat(uiConfig.S_HCO_init),
parseFloat(uiConfig.X_I_init),
parseFloat(uiConfig.X_S_init),
parseFloat(uiConfig.X_H_init),
parseFloat(uiConfig.X_STO_init),
parseFloat(uiConfig.X_A_init),
parseFloat(uiConfig.X_TS_init)
],
timeStep: parseFloat(uiConfig.timeStep)
}
}
/**
* Register this node as a child upstream and downstream.
* Delayed to avoid Node-RED startup race conditions.
*/
_registerChild() {
setTimeout(() => {
this.node.send([
null,
null,
{ topic: 'registerChild', payload: this.node.id, positionVsParent: this.config?.functionality?.positionVsParent || 'atEquipment' }
]);
}, 100);
}
/**
* Setup reactor class based on config
*/
_setupClass() {
let new_reactor;
switch (this.config.reactor_type) {
case "CSTR":
new_reactor = new Reactor_CSTR(this.config);
break;
case "PFR":
new_reactor = new Reactor_PFR(this.config);
break;
default:
console.warn("Unknown reactor type: " + uiConfig.reactor_type);
} }
return this._output.formatMsg(telemetry, this.config, 'influxdb'); this.source = new_reactor; // protect from reassignment
this.node.source = this.source;
}
_startTickLoop() {
setTimeout(() => {
this._tickInterval = setInterval(() => this._tick(), 1000);
}, 1000);
}
_tick(){
this.node.send([this.source.getEffluent, null, null]);
} }
_attachCloseHandler() { _attachCloseHandler() {
this.node.on('close', (done) => { this.node.on('close', (done) => {
clearInterval(this._tickInterval); clearInterval(this._tickInterval);
if (typeof done === 'function') done(); done();
}); });
} }
} }
module.exports = nodeClass; module.exports = nodeClass;

420
src/reaction_modules/asm3_class Koch.js
View File

@@ -1,211 +1,211 @@
const math = require('mathjs') const math = require('mathjs')
/** /**
* ASM3 class for the Activated Sludge Model No. 3 (ASM3). Using Koch et al. 2000 parameters. * ASM3 class for the Activated Sludge Model No. 3 (ASM3). Using Koch et al. 2000 parameters.
*/ */
class ASM3 { class ASM3 {
constructor() { constructor() {
/** /**
* Kinetic parameters for ASM3 at 20 C. Using Koch et al. 2000 parameters. * Kinetic parameters for ASM3 at 20 C. Using Koch et al. 2000 parameters.
* @property {Object} kin_params - Kinetic parameters * @property {Object} kin_params - Kinetic parameters
*/ */
this.kin_params = { this.kin_params = {
// Hydrolysis // Hydrolysis
k_H: 9., // hydrolysis rate constant [g X_S g-1 X_H d-1] k_H: 9., // hydrolysis rate constant [g X_S g-1 X_H d-1]
K_X: 1., // hydrolysis saturation constant [g X_S g-1 X_H] K_X: 1., // hydrolysis saturation constant [g X_S g-1 X_H]
// Heterotrophs // Heterotrophs
k_STO: 12., // storage rate constant [g S_S g-1 X_H d-1] k_STO: 12., // storage rate constant [g S_S g-1 X_H d-1]
nu_NO: 0.5, // anoxic reduction factor [-] nu_NO: 0.5, // anoxic reduction factor [-]
K_O: 0.2, // saturation constant S_0 [g O2 m-3] K_O: 0.2, // saturation constant S_0 [g O2 m-3]
K_NO: 0.5, // saturation constant S_NO [g NO3-N m-3] K_NO: 0.5, // saturation constant S_NO [g NO3-N m-3]
K_S: 10., // saturation constant S_s [g COD m-3] K_S: 10., // saturation constant S_s [g COD m-3]
K_STO: 0.1, // saturation constant X_STO [g X_STO g-1 X_H] K_STO: 0.1, // saturation constant X_STO [g X_STO g-1 X_H]
mu_H_max: 3., // maximum specific growth rate [d-1] mu_H_max: 3., // maximum specific growth rate [d-1]
K_NH: 0.01, // saturation constant S_NH3 [g NH3-N m-3] K_NH: 0.01, // saturation constant S_NH3 [g NH3-N m-3]
K_HCO: 0.1, // saturation constant S_HCO [mole HCO3 m-3] K_HCO: 0.1, // saturation constant S_HCO [mole HCO3 m-3]
b_H_O: 0.3, // aerobic respiration rate [d-1] b_H_O: 0.3, // aerobic respiration rate [d-1]
b_H_NO: 0.15, // anoxic respiration rate [d-1] b_H_NO: 0.15, // anoxic respiration rate [d-1]
b_STO_O: 0.3, // aerobic respitation rate X_STO [d-1] b_STO_O: 0.3, // aerobic respitation rate X_STO [d-1]
b_STO_NO: 0.15, // anoxic respitation rate X_STO [d-1] b_STO_NO: 0.15, // anoxic respitation rate X_STO [d-1]
// Autotrophs // Autotrophs
mu_A_max: 1.3, // maximum specific growth rate [d-1] mu_A_max: 1.3, // maximum specific growth rate [d-1]
K_A_NH: 1.4, // saturation constant S_NH3 [g NH3-N m-3] K_A_NH: 1.4, // saturation constant S_NH3 [g NH3-N m-3]
K_A_O: 0.5, // saturation constant S_0 [g O2 m-3] K_A_O: 0.5, // saturation constant S_0 [g O2 m-3]
K_A_HCO: 0.5, // saturation constant S_HCO [mole HCO3 m-3] K_A_HCO: 0.5, // saturation constant S_HCO [mole HCO3 m-3]
b_A_O: 0.20, // aerobic respiration rate [d-1] b_A_O: 0.20, // aerobic respiration rate [d-1]
b_A_NO: 0.10 // anoxic respiration rate [d-1] b_A_NO: 0.10 // anoxic respiration rate [d-1]
}; };
/** /**
* Stoichiometric and composition parameters for ASM3. Using Koch et al. 2000 parameters. * Stoichiometric and composition parameters for ASM3. Using Koch et al. 2000 parameters.
* @property {Object} stoi_params - Stoichiometric parameters * @property {Object} stoi_params - Stoichiometric parameters
*/ */
this.stoi_params = { this.stoi_params = {
// Fractions // Fractions
f_SI: 0., // fraction S_I from hydrolysis [g S_I g-1 X_S] f_SI: 0., // fraction S_I from hydrolysis [g S_I g-1 X_S]
f_XI: 0.2, // fraction X_I from decomp X_H [g X_I g-1 X_H] f_XI: 0.2, // fraction X_I from decomp X_H [g X_I g-1 X_H]
// Yields // Yields
Y_STO_O: 0.80, // aerobic yield X_STO per S_S [g X_STO g-1 S_S] Y_STO_O: 0.80, // aerobic yield X_STO per S_S [g X_STO g-1 S_S]
Y_STO_NO: 0.70, // anoxic yield X_STO per S_S [g X_STO g-1 S_S] Y_STO_NO: 0.70, // anoxic yield X_STO per S_S [g X_STO g-1 S_S]
Y_H_O: 0.80, // aerobic yield X_H per X_STO [g X_H g-1 X_STO] Y_H_O: 0.80, // aerobic yield X_H per X_STO [g X_H g-1 X_STO]
Y_H_NO: 0.65, // anoxic yield X_H per X_STO [g X_H g-1 X_STO] Y_H_NO: 0.65, // anoxic yield X_H per X_STO [g X_H g-1 X_STO]
Y_A: 0.24, // anoxic yield X_A per S_NO [g X_A g-1 NO3-N] Y_A: 0.24, // anoxic yield X_A per S_NO [g X_A g-1 NO3-N]
// Composition (COD via DoR) // Composition (COD via DoR)
i_CODN: -1.71, // COD content (DoR) [g COD g-1 N2-N] i_CODN: -1.71, // COD content (DoR) [g COD g-1 N2-N]
i_CODNO: -4.57, // COD content (DoR) [g COD g-1 NO3-N] i_CODNO: -4.57, // COD content (DoR) [g COD g-1 NO3-N]
// Composition (nitrogen) // Composition (nitrogen)
i_NSI: 0.01, // nitrogen content S_I [g N g-1 S_I] i_NSI: 0.01, // nitrogen content S_I [g N g-1 S_I]
i_NSS: 0.03, // nitrogen content S_S [g N g-1 S_S] i_NSS: 0.03, // nitrogen content S_S [g N g-1 S_S]
i_NXI: 0.04, // nitrogen content X_I [g N g-1 X_I] i_NXI: 0.04, // nitrogen content X_I [g N g-1 X_I]
i_NXS: 0.03, // nitrogen content X_S [g N g-1 X_S] i_NXS: 0.03, // nitrogen content X_S [g N g-1 X_S]
i_NBM: 0.07, // nitrogen content X_H / X_A [g N g-1 X_H / X_A] i_NBM: 0.07, // nitrogen content X_H / X_A [g N g-1 X_H / X_A]
// Composition (TSS) // Composition (TSS)
i_TSXI: 0.75, // TSS content X_I [g TS g-1 X_I] i_TSXI: 0.75, // TSS content X_I [g TS g-1 X_I]
i_TSXS: 0.75, // TSS content X_S [g TS g-1 X_S] i_TSXS: 0.75, // TSS content X_S [g TS g-1 X_S]
i_TSBM: 0.90, // TSS content X_H / X_A [g TS g-1 X_H / X_A] i_TSBM: 0.90, // TSS content X_H / X_A [g TS g-1 X_H / X_A]
i_TSSTO: 0.60, // TSS content X_STO (PHB based) [g TS g-1 X_STO] i_TSSTO: 0.60, // TSS content X_STO (PHB based) [g TS g-1 X_STO]
// Composition (charge) // Composition (charge)
i_cNH: 1/14, // charge per S_NH [mole H+ g-1 NH3-N] i_cNH: 1/14, // charge per S_NH [mole H+ g-1 NH3-N]
i_cNO: -1/14 // charge per S_NO [mole H+ g-1 NO3-N] i_cNO: -1/14 // charge per S_NO [mole H+ g-1 NO3-N]
}; };
/** /**
* Temperature theta parameters for ASM3. Using Koch et al. 2000 parameters. * Temperature theta parameters for ASM3. Using Koch et al. 2000 parameters.
* These parameters are used to adjust reaction rates based on temperature. * These parameters are used to adjust reaction rates based on temperature.
* @property {Object} temp_params - Temperature theta parameters * @property {Object} temp_params - Temperature theta parameters
*/ */
this.temp_params = { this.temp_params = {
// Hydrolysis // Hydrolysis
theta_H: 0.04, theta_H: 0.04,
// Heterotrophs // Heterotrophs
theta_STO: 0.07, theta_STO: 0.07,
theta_mu_H: 0.07, theta_mu_H: 0.07,
theta_b_H_O: 0.07, theta_b_H_O: 0.07,
theta_b_H_NO: 0.07, theta_b_H_NO: 0.07,
theta_b_STO_O: this._compute_theta(0.1, 0.3, 10, 20), theta_b_STO_O: this._compute_theta(0.1, 0.3, 10, 20),
theta_b_STO_NO: this._compute_theta(0.05, 0.15, 10, 20), theta_b_STO_NO: this._compute_theta(0.05, 0.15, 10, 20),
// Autotrophs // Autotrophs
theta_mu_A: 0.105, theta_mu_A: 0.105,
theta_b_A_O: 0.105, theta_b_A_O: 0.105,
theta_b_A_NO: 0.105 theta_b_A_NO: 0.105
}; };
this.stoi_matrix = this._initialise_stoi_matrix(); this.stoi_matrix = this._initialise_stoi_matrix();
} }
/** /**
* Initialises the stoichiometric matrix for ASM3. * Initialises the stoichiometric matrix for ASM3.
* @returns {Array} - The stoichiometric matrix for ASM3. (2D array) * @returns {Array} - The stoichiometric matrix for ASM3. (2D array)
*/ */
_initialise_stoi_matrix() { // initialise stoichiometric matrix _initialise_stoi_matrix() { // initialise stoichiometric matrix
const { f_SI, f_XI, Y_STO_O, Y_STO_NO, Y_H_O, Y_H_NO, Y_A, i_CODN, i_CODNO, i_NSI, i_NSS, i_NXI, i_NXS, i_NBM, i_TSXI, i_TSXS, i_TSBM, i_TSSTO, i_cNH, i_cNO } = this.stoi_params; const { f_SI, f_XI, Y_STO_O, Y_STO_NO, Y_H_O, Y_H_NO, Y_A, i_CODN, i_CODNO, i_NSI, i_NSS, i_NXI, i_NXS, i_NBM, i_TSXI, i_TSXS, i_TSBM, i_TSSTO, i_cNH, i_cNO } = this.stoi_params;
const stoi_matrix = Array(12); const stoi_matrix = Array(12);
// S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS // S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS
stoi_matrix[0] = [0., f_SI, 1.-f_SI, i_NXS-(1.-f_SI)*i_NSS-f_SI*i_NSI, 0., 0., (i_NXS-(1.-f_SI)*i_NSS-f_SI*i_NSI)*i_cNH, 0., -1., 0., 0., 0., -i_TSXS]; stoi_matrix[0] = [0., f_SI, 1.-f_SI, i_NXS-(1.-f_SI)*i_NSS-f_SI*i_NSI, 0., 0., (i_NXS-(1.-f_SI)*i_NSS-f_SI*i_NSI)*i_cNH, 0., -1., 0., 0., 0., -i_TSXS];
stoi_matrix[1] = [-(1.-Y_STO_O), 0, -1., i_NSS, 0., 0., i_NSS*i_cNH, 0., 0., 0., Y_STO_O, 0., Y_STO_O*i_TSSTO]; stoi_matrix[1] = [-(1.-Y_STO_O), 0, -1., i_NSS, 0., 0., i_NSS*i_cNH, 0., 0., 0., Y_STO_O, 0., Y_STO_O*i_TSSTO];
stoi_matrix[2] = [0., 0., -1., i_NSS, -(1.-Y_STO_NO)/(i_CODNO-i_CODN), (1.-Y_STO_NO)/(i_CODNO-i_CODN), i_NSS*i_cNH + (1.-Y_STO_NO)/(i_CODNO-i_CODN)*i_cNO, 0., 0., 0., Y_STO_NO, 0., Y_STO_NO*i_TSSTO]; stoi_matrix[2] = [0., 0., -1., i_NSS, -(1.-Y_STO_NO)/(i_CODNO-i_CODN), (1.-Y_STO_NO)/(i_CODNO-i_CODN), i_NSS*i_cNH + (1.-Y_STO_NO)/(i_CODNO-i_CODN)*i_cNO, 0., 0., 0., Y_STO_NO, 0., Y_STO_NO*i_TSSTO];
stoi_matrix[3] = [-(1.-Y_H_O)/Y_H_O, 0., 0., -i_NBM, 0., 0., -i_NBM*i_cNH, 0., 0., 1., -1./Y_H_O, 0., i_TSBM-i_TSSTO/Y_H_O]; stoi_matrix[3] = [-(1.-Y_H_O)/Y_H_O, 0., 0., -i_NBM, 0., 0., -i_NBM*i_cNH, 0., 0., 1., -1./Y_H_O, 0., i_TSBM-i_TSSTO/Y_H_O];
stoi_matrix[4] = [0., 0., 0., -i_NBM, -(1.-Y_H_NO)/(Y_H_NO*(i_CODNO-i_CODN)), (1.-Y_H_NO)/(Y_H_NO*(i_CODNO-i_CODN)), -i_NBM*i_cNH+(1.-Y_H_NO)/(Y_H_NO*(i_CODNO-i_CODN))*i_cNO, 0., 0., 1., -1./Y_H_NO, 0., i_TSBM-i_TSSTO/Y_H_NO]; stoi_matrix[4] = [0., 0., 0., -i_NBM, -(1.-Y_H_NO)/(Y_H_NO*(i_CODNO-i_CODN)), (1.-Y_H_NO)/(Y_H_NO*(i_CODNO-i_CODN)), -i_NBM*i_cNH+(1.-Y_H_NO)/(Y_H_NO*(i_CODNO-i_CODN))*i_cNO, 0., 0., 1., -1./Y_H_NO, 0., i_TSBM-i_TSSTO/Y_H_NO];
stoi_matrix[5] = [f_XI-1., 0., 0., i_NBM-f_XI*i_NXI, 0., 0., (i_NBM-f_XI*i_NXI)*i_cNH, f_XI, 0., -1., 0., 0., f_XI*i_TSXI-i_TSBM]; stoi_matrix[5] = [f_XI-1., 0., 0., i_NBM-f_XI*i_NXI, 0., 0., (i_NBM-f_XI*i_NXI)*i_cNH, f_XI, 0., -1., 0., 0., f_XI*i_TSXI-i_TSBM];
stoi_matrix[6] = [0., 0., 0., i_NBM-f_XI*i_NXI, -(1.-f_XI)/(i_CODNO-i_CODN), (1.-f_XI)/(i_CODNO-i_CODN), (i_NBM-f_XI*i_NXI)*i_cNH+(1-f_XI)/(i_CODNO-i_CODN)*i_cNO, f_XI, 0., -1., 0., 0., f_XI*i_TSXI-i_TSBM]; stoi_matrix[6] = [0., 0., 0., i_NBM-f_XI*i_NXI, -(1.-f_XI)/(i_CODNO-i_CODN), (1.-f_XI)/(i_CODNO-i_CODN), (i_NBM-f_XI*i_NXI)*i_cNH+(1-f_XI)/(i_CODNO-i_CODN)*i_cNO, f_XI, 0., -1., 0., 0., f_XI*i_TSXI-i_TSBM];
stoi_matrix[7] = [-1., 0., 0., 0., 0., 0., 0., 0., 0., 0., -1., 0., -i_TSSTO]; stoi_matrix[7] = [-1., 0., 0., 0., 0., 0., 0., 0., 0., 0., -1., 0., -i_TSSTO];
stoi_matrix[8] = [0., 0., 0., 0., -1./(i_CODNO-i_CODN), 1./(i_CODNO-i_CODN), i_cNO/(i_CODNO-i_CODN), 0., 0., 0., -1., 0., -i_TSSTO]; stoi_matrix[8] = [0., 0., 0., 0., -1./(i_CODNO-i_CODN), 1./(i_CODNO-i_CODN), i_cNO/(i_CODNO-i_CODN), 0., 0., 0., -1., 0., -i_TSSTO];
stoi_matrix[9] = [1.+i_CODNO/Y_A, 0., 0., -1./Y_A-i_NBM, 0., 1./Y_A, (-1./Y_A-i_NBM)*i_cNH+i_cNO/Y_A, 0., 0., 0., 0., 1., i_TSBM]; stoi_matrix[9] = [1.+i_CODNO/Y_A, 0., 0., -1./Y_A-i_NBM, 0., 1./Y_A, (-1./Y_A-i_NBM)*i_cNH+i_cNO/Y_A, 0., 0., 0., 0., 1., i_TSBM];
stoi_matrix[10] = [f_XI-1., 0., 0., i_NBM-f_XI*i_NXI, 0., 0., (i_NBM-f_XI*i_NXI)*i_cNH, f_XI, 0., 0., 0., -1., f_XI*i_TSXI-i_TSBM]; stoi_matrix[10] = [f_XI-1., 0., 0., i_NBM-f_XI*i_NXI, 0., 0., (i_NBM-f_XI*i_NXI)*i_cNH, f_XI, 0., 0., 0., -1., f_XI*i_TSXI-i_TSBM];
stoi_matrix[11] = [0., 0., 0., i_NBM-f_XI*i_NXI, -(1.-f_XI)/(i_CODNO-i_CODN), (1.-f_XI)/(i_CODNO-i_CODN), (i_NBM-f_XI*i_NXI)*i_cNH+(1-f_XI)/(i_CODNO-i_CODN)*i_cNO, 0., 0., 0., 0., -1., f_XI*i_TSXI-i_TSBM]; stoi_matrix[11] = [0., 0., 0., i_NBM-f_XI*i_NXI, -(1.-f_XI)/(i_CODNO-i_CODN), (1.-f_XI)/(i_CODNO-i_CODN), (i_NBM-f_XI*i_NXI)*i_cNH+(1-f_XI)/(i_CODNO-i_CODN)*i_cNO, 0., 0., 0., 0., -1., f_XI*i_TSXI-i_TSBM];
return stoi_matrix[0].map((col, i) => stoi_matrix.map(row => row[i])); // transpose matrix return stoi_matrix[0].map((col, i) => stoi_matrix.map(row => row[i])); // transpose matrix
} }
/** /**
* Computes the Monod equation rate value for a given concentration and half-saturation constant. * Computes the Monod equation rate value for a given concentration and half-saturation constant.
* @param {number} c - Concentration of reaction species. * @param {number} c - Concentration of reaction species.
* @param {number} K - Half-saturation constant for the reaction species. * @param {number} K - Half-saturation constant for the reaction species.
* @returns {number} - Monod equation rate value for the given concentration and half-saturation constant. * @returns {number} - Monod equation rate value for the given concentration and half-saturation constant.
*/ */
_monod(c, K) { _monod(c, K) {
return c / (K + c); return c / (K + c);
} }
/** /**
* Computes the inverse Monod equation rate value for a given concentration and half-saturation constant. Used for inhibition. * Computes the inverse Monod equation rate value for a given concentration and half-saturation constant. Used for inhibition.
* @param {number} c - Concentration of reaction species. * @param {number} c - Concentration of reaction species.
* @param {number} K - Half-saturation constant for the reaction species. * @param {number} K - Half-saturation constant for the reaction species.
* @returns {number} - Inverse Monod equation rate value for the given concentration and half-saturation constant. * @returns {number} - Inverse Monod equation rate value for the given concentration and half-saturation constant.
*/ */
_inv_monod(c, K) { _inv_monod(c, K) {
return K / (K + c); return K / (K + c);
} }
/** /**
* Adjust the rate parameter for temperature T using simplied Arrhenius equation based on rate constant at 20 degrees Celsius and theta parameter. * Adjust the rate parameter for temperature T using simplied Arrhenius equation based on rate constant at 20 degrees Celsius and theta parameter.
* @param {number} k - Rate constant at 20 degrees Celcius. * @param {number} k - Rate constant at 20 degrees Celcius.
* @param {number} theta - Theta parameter. * @param {number} theta - Theta parameter.
* @param {number} T - Temperature in Celcius. * @param {number} T - Temperature in Celcius.
* @returns {number} - Adjusted rate parameter at temperature T based on the Arrhenius equation. * @returns {number} - Adjusted rate parameter at temperature T based on the Arrhenius equation.
*/ */
_arrhenius(k, theta, T) { _arrhenius(k, theta, T) {
return k * Math.exp(theta*(T-20)); return k * Math.exp(theta*(T-20));
} }
/** /**
* Computes the temperature theta parameter based on two rate constants and their corresponding temperatures. * Computes the temperature theta parameter based on two rate constants and their corresponding temperatures.
* @param {number} k1 - Rate constant at temperature T1. * @param {number} k1 - Rate constant at temperature T1.
* @param {number} k2 - Rate constant at temperature T2. * @param {number} k2 - Rate constant at temperature T2.
* @param {number} T1 - Temperature T1 in Celcius. * @param {number} T1 - Temperature T1 in Celcius.
* @param {number} T2 - Temperature T2 in Celcius. * @param {number} T2 - Temperature T2 in Celcius.
* @returns {number} - Theta parameter. * @returns {number} - Theta parameter.
*/ */
_compute_theta(k1, k2, T1, T2) { _compute_theta(k1, k2, T1, T2) {
return Math.log(k1/k2)/(T1-T2); return Math.log(k1/k2)/(T1-T2);
} }
/** /**
* Computes the reaction rates for each process reaction based on the current state and temperature. * Computes the reaction rates for each process reaction based on the current state and temperature.
* @param {Array} state - State vector containing concentrations of reaction species. * @param {Array} state - State vector containing concentrations of reaction species.
* @param {number} [T=20] - Temperature in degrees Celsius (default is 20). * @param {number} [T=20] - Temperature in degrees Celsius (default is 20).
* @returns {Array} - Reaction rates for each process reaction. * @returns {Array} - Reaction rates for each process reaction.
*/ */
compute_rates(state, T = 20) { compute_rates(state, T = 20) {
// state: S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS // state: S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS
const rates = Array(12); const rates = Array(12);
const [S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS] = state; const [S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS] = state;
const { k_H, K_X, k_STO, nu_NO, K_O, K_NO, K_S, K_STO, mu_H_max, K_NH, K_HCO, b_H_O, b_H_NO, b_STO_O, b_STO_NO, mu_A_max, K_A_NH, K_A_O, K_A_HCO, b_A_O, b_A_NO } = this.kin_params; const { k_H, K_X, k_STO, nu_NO, K_O, K_NO, K_S, K_STO, mu_H_max, K_NH, K_HCO, b_H_O, b_H_NO, b_STO_O, b_STO_NO, mu_A_max, K_A_NH, K_A_O, K_A_HCO, b_A_O, b_A_NO } = this.kin_params;
const { theta_H, theta_STO, theta_mu_H, theta_b_H_O, theta_b_H_NO, theta_b_STO_O, theta_b_STO_NO, theta_mu_A, theta_b_A_O, theta_b_A_NO } = this.temp_params; const { theta_H, theta_STO, theta_mu_H, theta_b_H_O, theta_b_H_NO, theta_b_STO_O, theta_b_STO_NO, theta_mu_A, theta_b_A_O, theta_b_A_NO } = this.temp_params;
// Hydrolysis // Hydrolysis
rates[0] = X_H == 0 ? 0 : this._arrhenius(k_H, theta_H, T) * this._monod(X_S / X_H, K_X) * X_H; rates[0] = X_H == 0 ? 0 : this._arrhenius(k_H, theta_H, T) * this._monod(X_S / X_H, K_X) * X_H;
// Heterotrophs // Heterotrophs
rates[1] = this._arrhenius(k_STO, theta_STO, T) * this._monod(S_O, K_O) * this._monod(S_S, K_S) * X_H; rates[1] = this._arrhenius(k_STO, theta_STO, T) * this._monod(S_O, K_O) * this._monod(S_S, K_S) * X_H;
rates[2] = this._arrhenius(k_STO, theta_STO, T) * nu_NO * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * this._monod(S_S, K_S) * X_H; rates[2] = this._arrhenius(k_STO, theta_STO, T) * nu_NO * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * this._monod(S_S, K_S) * X_H;
rates[3] = X_H == 0 ? 0 : this._arrhenius(mu_H_max, theta_mu_H, T) * this._monod(S_O, K_O) * this._monod(S_NH, K_NH) * this._monod(S_HCO, K_HCO) * this._monod(X_STO/X_H, K_STO) * X_H; rates[3] = X_H == 0 ? 0 : this._arrhenius(mu_H_max, theta_mu_H, T) * this._monod(S_O, K_O) * this._monod(S_NH, K_NH) * this._monod(S_HCO, K_HCO) * this._monod(X_STO/X_H, K_STO) * X_H;
rates[4] = X_H == 0 ? 0 : this._arrhenius(mu_H_max, theta_mu_H, T) * nu_NO * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * this._monod(S_NH, K_NH) * this._monod(S_HCO, K_HCO) * this._monod(X_STO/X_H, K_STO) * X_H; rates[4] = X_H == 0 ? 0 : this._arrhenius(mu_H_max, theta_mu_H, T) * nu_NO * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * this._monod(S_NH, K_NH) * this._monod(S_HCO, K_HCO) * this._monod(X_STO/X_H, K_STO) * X_H;
rates[5] = this._arrhenius(b_H_O, theta_b_H_O, T) * this._monod(S_O, K_O) * X_H; rates[5] = this._arrhenius(b_H_O, theta_b_H_O, T) * this._monod(S_O, K_O) * X_H;
rates[6] = this._arrhenius(b_H_NO, theta_b_H_NO, T) * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * X_H; rates[6] = this._arrhenius(b_H_NO, theta_b_H_NO, T) * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * X_H;
rates[7] = this._arrhenius(b_STO_O, theta_b_STO_O, T) * this._monod(S_O, K_O) * X_H; rates[7] = this._arrhenius(b_STO_O, theta_b_STO_O, T) * this._monod(S_O, K_O) * X_H;
rates[8] = this._arrhenius(b_STO_NO, theta_b_STO_NO, T) * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * X_STO; rates[8] = this._arrhenius(b_STO_NO, theta_b_STO_NO, T) * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * X_STO;
// Autotrophs // Autotrophs
rates[9] = this._arrhenius(mu_A_max, theta_mu_A, T) * this._monod(S_O, K_A_O) * this._monod(S_NH, K_A_NH) * this._monod(S_HCO, K_A_HCO) * X_A; rates[9] = this._arrhenius(mu_A_max, theta_mu_A, T) * this._monod(S_O, K_A_O) * this._monod(S_NH, K_A_NH) * this._monod(S_HCO, K_A_HCO) * X_A;
rates[10] = this._arrhenius(b_A_O, theta_b_A_O, T) * this._monod(S_O, K_O) * X_A; rates[10] = this._arrhenius(b_A_O, theta_b_A_O, T) * this._monod(S_O, K_O) * X_A;
rates[11] = this._arrhenius(b_A_NO, theta_b_A_NO, T) * this._inv_monod(S_O, K_A_O) * this._monod(S_NO, K_NO) * X_A; rates[11] = this._arrhenius(b_A_NO, theta_b_A_NO, T) * this._inv_monod(S_O, K_A_O) * this._monod(S_NO, K_NO) * X_A;
return rates; return rates;
} }
/** /**
* Computes the change in concentrations of reaction species based on the current state and temperature. * Computes the change in concentrations of reaction species based on the current state and temperature.
* @param {Array} state - State vector containing concentrations of reaction species. * @param {Array} state - State vector containing concentrations of reaction species.
* @param {number} [T=20] - Temperature in degrees Celsius (default is 20). * @param {number} [T=20] - Temperature in degrees Celsius (default is 20).
* @returns {Array} - Change in reaction species concentrations. * @returns {Array} - Change in reaction species concentrations.
*/ */
compute_dC(state, T = 20) { // compute changes in concentrations compute_dC(state, T = 20) { // compute changes in concentrations
// state: S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS // state: S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS
return math.multiply(this.stoi_matrix, this.compute_rates(state, T)); return math.multiply(this.stoi_matrix, this.compute_rates(state, T));
} }
} }
module.exports = ASM3; module.exports = ASM3;

420
src/reaction_modules/asm3_class.js
View File

@@ -1,211 +1,211 @@
const math = require('mathjs') const math = require('mathjs')
/** /**
* ASM3 class for the Activated Sludge Model No. 3 (ASM3). * ASM3 class for the Activated Sludge Model No. 3 (ASM3).
*/ */
class ASM3 { class ASM3 {
constructor() { constructor() {
/** /**
* Kinetic parameters for ASM3 at 20 C. * Kinetic parameters for ASM3 at 20 C.
* @property {Object} kin_params - Kinetic parameters * @property {Object} kin_params - Kinetic parameters
*/ */
this.kin_params = { this.kin_params = {
// Hydrolysis // Hydrolysis
k_H: 3., // hydrolysis rate constant [g X_S g-1 X_H d-1] k_H: 3., // hydrolysis rate constant [g X_S g-1 X_H d-1]
K_X: 1., // hydrolysis saturation constant [g X_S g-1 X_H] K_X: 1., // hydrolysis saturation constant [g X_S g-1 X_H]
// Heterotrophs // Heterotrophs
k_STO: 5., // storage rate constant [g S_S g-1 X_H d-1] k_STO: 5., // storage rate constant [g S_S g-1 X_H d-1]
nu_NO: 0.6, // anoxic reduction factor [-] nu_NO: 0.6, // anoxic reduction factor [-]
K_O: 0.2, // saturation constant S_0 [g O2 m-3] K_O: 0.2, // saturation constant S_0 [g O2 m-3]
K_NO: 0.5, // saturation constant S_NO [g NO3-N m-3] K_NO: 0.5, // saturation constant S_NO [g NO3-N m-3]
K_S: 2., // saturation constant S_s [g COD m-3] K_S: 2., // saturation constant S_s [g COD m-3]
K_STO: 1., // saturation constant X_STO [g X_STO g-1 X_H] K_STO: 1., // saturation constant X_STO [g X_STO g-1 X_H]
mu_H_max: 2., // maximum specific growth rate [d-1] mu_H_max: 2., // maximum specific growth rate [d-1]
K_NH: 0.01, // saturation constant S_NH3 [g NH3-N m-3] K_NH: 0.01, // saturation constant S_NH3 [g NH3-N m-3]
K_HCO: 0.1, // saturation constant S_HCO [mole HCO3 m-3] K_HCO: 0.1, // saturation constant S_HCO [mole HCO3 m-3]
b_H_O: 0.2, // aerobic respiration rate [d-1] b_H_O: 0.2, // aerobic respiration rate [d-1]
b_H_NO: 0.1, // anoxic respiration rate [d-1] b_H_NO: 0.1, // anoxic respiration rate [d-1]
b_STO_O: 0.2, // aerobic respitation rate X_STO [d-1] b_STO_O: 0.2, // aerobic respitation rate X_STO [d-1]
b_STO_NO: 0.1, // anoxic respitation rate X_STO [d-1] b_STO_NO: 0.1, // anoxic respitation rate X_STO [d-1]
// Autotrophs // Autotrophs
mu_A_max: 1.0, // maximum specific growth rate [d-1] mu_A_max: 1.0, // maximum specific growth rate [d-1]
K_A_NH: 1., // saturation constant S_NH3 [g NH3-N m-3] K_A_NH: 1., // saturation constant S_NH3 [g NH3-N m-3]
K_A_O: 0.5, // saturation constant S_0 [g O2 m-3] K_A_O: 0.5, // saturation constant S_0 [g O2 m-3]
K_A_HCO: 0.5, // saturation constant S_HCO [mole HCO3 m-3] K_A_HCO: 0.5, // saturation constant S_HCO [mole HCO3 m-3]
b_A_O: 0.15, // aerobic respiration rate [d-1] b_A_O: 0.15, // aerobic respiration rate [d-1]
b_A_NO: 0.05 // anoxic respiration rate [d-1] b_A_NO: 0.05 // anoxic respiration rate [d-1]
}; };
/** /**
* Stoichiometric and composition parameters for ASM3. * Stoichiometric and composition parameters for ASM3.
* @property {Object} stoi_params - Stoichiometric parameters * @property {Object} stoi_params - Stoichiometric parameters
*/ */
this.stoi_params = { this.stoi_params = {
// Fractions // Fractions
f_SI: 0., // fraction S_I from hydrolysis [g S_I g-1 X_S] f_SI: 0., // fraction S_I from hydrolysis [g S_I g-1 X_S]
f_XI: 0.2, // fraction X_I from decomp X_H [g X_I g-1 X_H] f_XI: 0.2, // fraction X_I from decomp X_H [g X_I g-1 X_H]
// Yields // Yields
Y_STO_O: 0.85, // aerobic yield X_STO per S_S [g X_STO g-1 S_S] Y_STO_O: 0.85, // aerobic yield X_STO per S_S [g X_STO g-1 S_S]
Y_STO_NO: 0.80, // anoxic yield X_STO per S_S [g X_STO g-1 S_S] Y_STO_NO: 0.80, // anoxic yield X_STO per S_S [g X_STO g-1 S_S]
Y_H_O: 0.63, // aerobic yield X_H per X_STO [g X_H g-1 X_STO] Y_H_O: 0.63, // aerobic yield X_H per X_STO [g X_H g-1 X_STO]
Y_H_NO: 0.54, // anoxic yield X_H per X_STO [g X_H g-1 X_STO] Y_H_NO: 0.54, // anoxic yield X_H per X_STO [g X_H g-1 X_STO]
Y_A: 0.24, // anoxic yield X_A per S_NO [g X_A g-1 NO3-N] Y_A: 0.24, // anoxic yield X_A per S_NO [g X_A g-1 NO3-N]
// Composition (COD via DoR) // Composition (COD via DoR)
i_CODN: -1.71, // COD content (DoR) [g COD g-1 N2-N] i_CODN: -1.71, // COD content (DoR) [g COD g-1 N2-N]
i_CODNO: -4.57, // COD content (DoR) [g COD g-1 NO3-N] i_CODNO: -4.57, // COD content (DoR) [g COD g-1 NO3-N]
// Composition (nitrogen) // Composition (nitrogen)
i_NSI: 0.01, // nitrogen content S_I [g N g-1 S_I] i_NSI: 0.01, // nitrogen content S_I [g N g-1 S_I]
i_NSS: 0.03, // nitrogen content S_S [g N g-1 S_S] i_NSS: 0.03, // nitrogen content S_S [g N g-1 S_S]
i_NXI: 0.02, // nitrogen content X_I [g N g-1 X_I] i_NXI: 0.02, // nitrogen content X_I [g N g-1 X_I]
i_NXS: 0.04, // nitrogen content X_S [g N g-1 X_S] i_NXS: 0.04, // nitrogen content X_S [g N g-1 X_S]
i_NBM: 0.07, // nitrogen content X_H / X_A [g N g-1 X_H / X_A] i_NBM: 0.07, // nitrogen content X_H / X_A [g N g-1 X_H / X_A]
// Composition (TSS) // Composition (TSS)
i_TSXI: 0.75, // TSS content X_I [g TS g-1 X_I] i_TSXI: 0.75, // TSS content X_I [g TS g-1 X_I]
i_TSXS: 0.75, // TSS content X_S [g TS g-1 X_S] i_TSXS: 0.75, // TSS content X_S [g TS g-1 X_S]
i_TSBM: 0.90, // TSS content X_H / X_A [g TS g-1 X_H / X_A] i_TSBM: 0.90, // TSS content X_H / X_A [g TS g-1 X_H / X_A]
i_TSSTO: 0.60, // TSS content X_STO (PHB based) [g TS g-1 X_STO] i_TSSTO: 0.60, // TSS content X_STO (PHB based) [g TS g-1 X_STO]
// Composition (charge) // Composition (charge)
i_cNH: 1/14, // charge per S_NH [mole H+ g-1 NH3-N] i_cNH: 1/14, // charge per S_NH [mole H+ g-1 NH3-N]
i_cNO: -1/14 // charge per S_NO [mole H+ g-1 NO3-N] i_cNO: -1/14 // charge per S_NO [mole H+ g-1 NO3-N]
}; };
/** /**
* Temperature theta parameters for ASM3. * Temperature theta parameters for ASM3.
* These parameters are used to adjust reaction rates based on temperature. * These parameters are used to adjust reaction rates based on temperature.
* @property {Object} temp_params - Temperature theta parameters * @property {Object} temp_params - Temperature theta parameters
*/ */
this.temp_params = { this.temp_params = {
// Hydrolysis // Hydrolysis
theta_H: this._compute_theta(2, 3, 10, 20), theta_H: this._compute_theta(2, 3, 10, 20),
// Heterotrophs // Heterotrophs
theta_STO: this._compute_theta(2.5, 5, 10, 20), theta_STO: this._compute_theta(2.5, 5, 10, 20),
theta_mu_H: this._compute_theta(1, 2, 10, 20), theta_mu_H: this._compute_theta(1, 2, 10, 20),
theta_b_H_O: this._compute_theta(0.1, 0.2, 10, 20), theta_b_H_O: this._compute_theta(0.1, 0.2, 10, 20),
theta_b_H_NO: this._compute_theta(0.05, 0.1, 10, 20), theta_b_H_NO: this._compute_theta(0.05, 0.1, 10, 20),
theta_b_STO_O: this._compute_theta(0.1, 0.2, 10, 20), theta_b_STO_O: this._compute_theta(0.1, 0.2, 10, 20),
theta_b_STO_NO: this._compute_theta(0.05, 0.1, 10, 20), theta_b_STO_NO: this._compute_theta(0.05, 0.1, 10, 20),
// Autotrophs // Autotrophs
theta_mu_A: this._compute_theta(0.35, 1, 10, 20), theta_mu_A: this._compute_theta(0.35, 1, 10, 20),
theta_b_A_O: this._compute_theta(0.05, 0.15, 10, 20), theta_b_A_O: this._compute_theta(0.05, 0.15, 10, 20),
theta_b_A_NO: this._compute_theta(0.02, 0.05, 10, 20) theta_b_A_NO: this._compute_theta(0.02, 0.05, 10, 20)
}; };
this.stoi_matrix = this._initialise_stoi_matrix(); this.stoi_matrix = this._initialise_stoi_matrix();
} }
/** /**
* Initialises the stoichiometric matrix for ASM3. * Initialises the stoichiometric matrix for ASM3.
* @returns {Array} - The stoichiometric matrix for ASM3. (2D array) * @returns {Array} - The stoichiometric matrix for ASM3. (2D array)
*/ */
_initialise_stoi_matrix() { // initialise stoichiometric matrix _initialise_stoi_matrix() { // initialise stoichiometric matrix
const { f_SI, f_XI, Y_STO_O, Y_STO_NO, Y_H_O, Y_H_NO, Y_A, i_CODN, i_CODNO, i_NSI, i_NSS, i_NXI, i_NXS, i_NBM, i_TSXI, i_TSXS, i_TSBM, i_TSSTO, i_cNH, i_cNO } = this.stoi_params; const { f_SI, f_XI, Y_STO_O, Y_STO_NO, Y_H_O, Y_H_NO, Y_A, i_CODN, i_CODNO, i_NSI, i_NSS, i_NXI, i_NXS, i_NBM, i_TSXI, i_TSXS, i_TSBM, i_TSSTO, i_cNH, i_cNO } = this.stoi_params;
const stoi_matrix = Array(12); const stoi_matrix = Array(12);
// S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS // S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS
stoi_matrix[0] = [0., f_SI, 1.-f_SI, i_NXS-(1.-f_SI)*i_NSS-f_SI*i_NSI, 0., 0., (i_NXS-(1.-f_SI)*i_NSS-f_SI*i_NSI)*i_cNH, 0., -1., 0., 0., 0., -i_TSXS]; stoi_matrix[0] = [0., f_SI, 1.-f_SI, i_NXS-(1.-f_SI)*i_NSS-f_SI*i_NSI, 0., 0., (i_NXS-(1.-f_SI)*i_NSS-f_SI*i_NSI)*i_cNH, 0., -1., 0., 0., 0., -i_TSXS];
stoi_matrix[1] = [-(1.-Y_STO_O), 0, -1., i_NSS, 0., 0., i_NSS*i_cNH, 0., 0., 0., Y_STO_O, 0., Y_STO_O*i_TSSTO]; stoi_matrix[1] = [-(1.-Y_STO_O), 0, -1., i_NSS, 0., 0., i_NSS*i_cNH, 0., 0., 0., Y_STO_O, 0., Y_STO_O*i_TSSTO];
stoi_matrix[2] = [0., 0., -1., i_NSS, -(1.-Y_STO_NO)/(i_CODNO-i_CODN), (1.-Y_STO_NO)/(i_CODNO-i_CODN), i_NSS*i_cNH + (1.-Y_STO_NO)/(i_CODNO-i_CODN)*i_cNO, 0., 0., 0., Y_STO_NO, 0., Y_STO_NO*i_TSSTO]; stoi_matrix[2] = [0., 0., -1., i_NSS, -(1.-Y_STO_NO)/(i_CODNO-i_CODN), (1.-Y_STO_NO)/(i_CODNO-i_CODN), i_NSS*i_cNH + (1.-Y_STO_NO)/(i_CODNO-i_CODN)*i_cNO, 0., 0., 0., Y_STO_NO, 0., Y_STO_NO*i_TSSTO];
stoi_matrix[3] = [-(1.-Y_H_O)/Y_H_O, 0., 0., -i_NBM, 0., 0., -i_NBM*i_cNH, 0., 0., 1., -1./Y_H_O, 0., i_TSBM-i_TSSTO/Y_H_O]; stoi_matrix[3] = [-(1.-Y_H_O)/Y_H_O, 0., 0., -i_NBM, 0., 0., -i_NBM*i_cNH, 0., 0., 1., -1./Y_H_O, 0., i_TSBM-i_TSSTO/Y_H_O];
stoi_matrix[4] = [0., 0., 0., -i_NBM, -(1.-Y_H_NO)/(Y_H_NO*(i_CODNO-i_CODN)), (1.-Y_H_NO)/(Y_H_NO*(i_CODNO-i_CODN)), -i_NBM*i_cNH+(1.-Y_H_NO)/(Y_H_NO*(i_CODNO-i_CODN))*i_cNO, 0., 0., 1., -1./Y_H_NO, 0., i_TSBM-i_TSSTO/Y_H_NO]; stoi_matrix[4] = [0., 0., 0., -i_NBM, -(1.-Y_H_NO)/(Y_H_NO*(i_CODNO-i_CODN)), (1.-Y_H_NO)/(Y_H_NO*(i_CODNO-i_CODN)), -i_NBM*i_cNH+(1.-Y_H_NO)/(Y_H_NO*(i_CODNO-i_CODN))*i_cNO, 0., 0., 1., -1./Y_H_NO, 0., i_TSBM-i_TSSTO/Y_H_NO];
stoi_matrix[5] = [f_XI-1., 0., 0., i_NBM-f_XI*i_NXI, 0., 0., (i_NBM-f_XI*i_NXI)*i_cNH, f_XI, 0., -1., 0., 0., f_XI*i_TSXI-i_TSBM]; stoi_matrix[5] = [f_XI-1., 0., 0., i_NBM-f_XI*i_NXI, 0., 0., (i_NBM-f_XI*i_NXI)*i_cNH, f_XI, 0., -1., 0., 0., f_XI*i_TSXI-i_TSBM];
stoi_matrix[6] = [0., 0., 0., i_NBM-f_XI*i_NXI, -(1.-f_XI)/(i_CODNO-i_CODN), (1.-f_XI)/(i_CODNO-i_CODN), (i_NBM-f_XI*i_NXI)*i_cNH+(1-f_XI)/(i_CODNO-i_CODN)*i_cNO, f_XI, 0., -1., 0., 0., f_XI*i_TSXI-i_TSBM]; stoi_matrix[6] = [0., 0., 0., i_NBM-f_XI*i_NXI, -(1.-f_XI)/(i_CODNO-i_CODN), (1.-f_XI)/(i_CODNO-i_CODN), (i_NBM-f_XI*i_NXI)*i_cNH+(1-f_XI)/(i_CODNO-i_CODN)*i_cNO, f_XI, 0., -1., 0., 0., f_XI*i_TSXI-i_TSBM];
stoi_matrix[7] = [-1., 0., 0., 0., 0., 0., 0., 0., 0., 0., -1., 0., -i_TSSTO]; stoi_matrix[7] = [-1., 0., 0., 0., 0., 0., 0., 0., 0., 0., -1., 0., -i_TSSTO];
stoi_matrix[8] = [0., 0., 0., 0., -1./(i_CODNO-i_CODN), 1./(i_CODNO-i_CODN), i_cNO/(i_CODNO-i_CODN), 0., 0., 0., -1., 0., -i_TSSTO]; stoi_matrix[8] = [0., 0., 0., 0., -1./(i_CODNO-i_CODN), 1./(i_CODNO-i_CODN), i_cNO/(i_CODNO-i_CODN), 0., 0., 0., -1., 0., -i_TSSTO];
stoi_matrix[9] = [1.+i_CODNO/Y_A, 0., 0., -1./Y_A-i_NBM, 0., 1./Y_A, (-1./Y_A-i_NBM)*i_cNH+i_cNO/Y_A, 0., 0., 0., 0., 1., i_TSBM]; stoi_matrix[9] = [1.+i_CODNO/Y_A, 0., 0., -1./Y_A-i_NBM, 0., 1./Y_A, (-1./Y_A-i_NBM)*i_cNH+i_cNO/Y_A, 0., 0., 0., 0., 1., i_TSBM];
stoi_matrix[10] = [f_XI-1., 0., 0., i_NBM-f_XI*i_NXI, 0., 0., (i_NBM-f_XI*i_NXI)*i_cNH, f_XI, 0., 0., 0., -1., f_XI*i_TSXI-i_TSBM]; stoi_matrix[10] = [f_XI-1., 0., 0., i_NBM-f_XI*i_NXI, 0., 0., (i_NBM-f_XI*i_NXI)*i_cNH, f_XI, 0., 0., 0., -1., f_XI*i_TSXI-i_TSBM];
stoi_matrix[11] = [0., 0., 0., i_NBM-f_XI*i_NXI, -(1.-f_XI)/(i_CODNO-i_CODN), (1.-f_XI)/(i_CODNO-i_CODN), (i_NBM-f_XI*i_NXI)*i_cNH+(1-f_XI)/(i_CODNO-i_CODN)*i_cNO, 0., 0., 0., 0., -1., f_XI*i_TSXI-i_TSBM]; stoi_matrix[11] = [0., 0., 0., i_NBM-f_XI*i_NXI, -(1.-f_XI)/(i_CODNO-i_CODN), (1.-f_XI)/(i_CODNO-i_CODN), (i_NBM-f_XI*i_NXI)*i_cNH+(1-f_XI)/(i_CODNO-i_CODN)*i_cNO, 0., 0., 0., 0., -1., f_XI*i_TSXI-i_TSBM];
return stoi_matrix[0].map((col, i) => stoi_matrix.map(row => row[i])); // transpose matrix return stoi_matrix[0].map((col, i) => stoi_matrix.map(row => row[i])); // transpose matrix
} }
/** /**
* Computes the Monod equation rate value for a given concentration and half-saturation constant. * Computes the Monod equation rate value for a given concentration and half-saturation constant.
* @param {number} c - Concentration of reaction species. * @param {number} c - Concentration of reaction species.
* @param {number} K - Half-saturation constant for the reaction species. * @param {number} K - Half-saturation constant for the reaction species.
* @returns {number} - Monod equation rate value for the given concentration and half-saturation constant. * @returns {number} - Monod equation rate value for the given concentration and half-saturation constant.
*/ */
_monod(c, K) { _monod(c, K) {
return c / (K + c); return c / (K + c);
} }
/** /**
* Computes the inverse Monod equation rate value for a given concentration and half-saturation constant. Used for inhibition. * Computes the inverse Monod equation rate value for a given concentration and half-saturation constant. Used for inhibition.
* @param {number} c - Concentration of reaction species. * @param {number} c - Concentration of reaction species.
* @param {number} K - Half-saturation constant for the reaction species. * @param {number} K - Half-saturation constant for the reaction species.
* @returns {number} - Inverse Monod equation rate value for the given concentration and half-saturation constant. * @returns {number} - Inverse Monod equation rate value for the given concentration and half-saturation constant.
*/ */
_inv_monod(c, K) { _inv_monod(c, K) {
return K / (K + c); return K / (K + c);
} }
/** /**
* Adjust the rate parameter for temperature T using simplied Arrhenius equation based on rate constant at 20 degrees Celsius and theta parameter. * Adjust the rate parameter for temperature T using simplied Arrhenius equation based on rate constant at 20 degrees Celsius and theta parameter.
* @param {number} k - Rate constant at 20 degrees Celcius. * @param {number} k - Rate constant at 20 degrees Celcius.
* @param {number} theta - Theta parameter. * @param {number} theta - Theta parameter.
* @param {number} T - Temperature in Celcius. * @param {number} T - Temperature in Celcius.
* @returns {number} - Adjusted rate parameter at temperature T based on the Arrhenius equation. * @returns {number} - Adjusted rate parameter at temperature T based on the Arrhenius equation.
*/ */
_arrhenius(k, theta, T) { _arrhenius(k, theta, T) {
return k * Math.exp(theta*(T-20)); return k * Math.exp(theta*(T-20));
} }
/** /**
* Computes the temperature theta parameter based on two rate constants and their corresponding temperatures. * Computes the temperature theta parameter based on two rate constants and their corresponding temperatures.
* @param {number} k1 - Rate constant at temperature T1. * @param {number} k1 - Rate constant at temperature T1.
* @param {number} k2 - Rate constant at temperature T2. * @param {number} k2 - Rate constant at temperature T2.
* @param {number} T1 - Temperature T1 in Celcius. * @param {number} T1 - Temperature T1 in Celcius.
* @param {number} T2 - Temperature T2 in Celcius. * @param {number} T2 - Temperature T2 in Celcius.
* @returns {number} - Theta parameter. * @returns {number} - Theta parameter.
*/ */
_compute_theta(k1, k2, T1, T2) { _compute_theta(k1, k2, T1, T2) {
return Math.log(k1/k2)/(T1-T2); return Math.log(k1/k2)/(T1-T2);
} }
/** /**
* Computes the reaction rates for each process reaction based on the current state and temperature. * Computes the reaction rates for each process reaction based on the current state and temperature.
* @param {Array} state - State vector containing concentrations of reaction species. * @param {Array} state - State vector containing concentrations of reaction species.
* @param {number} [T=20] - Temperature in degrees Celsius (default is 20). * @param {number} [T=20] - Temperature in degrees Celsius (default is 20).
* @returns {Array} - Reaction rates for each process reaction. * @returns {Array} - Reaction rates for each process reaction.
*/ */
compute_rates(state, T = 20) { compute_rates(state, T = 20) {
// state: S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS // state: S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS
const rates = Array(12); const rates = Array(12);
const [S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS] = state; const [S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS] = state;
const { k_H, K_X, k_STO, nu_NO, K_O, K_NO, K_S, K_STO, mu_H_max, K_NH, K_HCO, b_H_O, b_H_NO, b_STO_O, b_STO_NO, mu_A_max, K_A_NH, K_A_O, K_A_HCO, b_A_O, b_A_NO } = this.kin_params; const { k_H, K_X, k_STO, nu_NO, K_O, K_NO, K_S, K_STO, mu_H_max, K_NH, K_HCO, b_H_O, b_H_NO, b_STO_O, b_STO_NO, mu_A_max, K_A_NH, K_A_O, K_A_HCO, b_A_O, b_A_NO } = this.kin_params;
const { theta_H, theta_STO, theta_mu_H, theta_b_H_O, theta_b_H_NO, theta_b_STO_O, theta_b_STO_NO, theta_mu_A, theta_b_A_O, theta_b_A_NO } = this.temp_params; const { theta_H, theta_STO, theta_mu_H, theta_b_H_O, theta_b_H_NO, theta_b_STO_O, theta_b_STO_NO, theta_mu_A, theta_b_A_O, theta_b_A_NO } = this.temp_params;
// Hydrolysis // Hydrolysis
rates[0] = X_H == 0 ? 0 : this._arrhenius(k_H, theta_H, T) * this._monod(X_S / X_H, K_X) * X_H; rates[0] = X_H == 0 ? 0 : this._arrhenius(k_H, theta_H, T) * this._monod(X_S / X_H, K_X) * X_H;
// Heterotrophs // Heterotrophs
rates[1] = this._arrhenius(k_STO, theta_STO, T) * this._monod(S_O, K_O) * this._monod(S_S, K_S) * X_H; rates[1] = this._arrhenius(k_STO, theta_STO, T) * this._monod(S_O, K_O) * this._monod(S_S, K_S) * X_H;
rates[2] = this._arrhenius(k_STO, theta_STO, T) * nu_NO * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * this._monod(S_S, K_S) * X_H; rates[2] = this._arrhenius(k_STO, theta_STO, T) * nu_NO * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * this._monod(S_S, K_S) * X_H;
rates[3] = X_H == 0 ? 0 : this._arrhenius(mu_H_max, theta_mu_H, T) * this._monod(S_O, K_O) * this._monod(S_NH, K_NH) * this._monod(S_HCO, K_HCO) * this._monod(X_STO/X_H, K_STO) * X_H; rates[3] = X_H == 0 ? 0 : this._arrhenius(mu_H_max, theta_mu_H, T) * this._monod(S_O, K_O) * this._monod(S_NH, K_NH) * this._monod(S_HCO, K_HCO) * this._monod(X_STO/X_H, K_STO) * X_H;
rates[4] = X_H == 0 ? 0 : this._arrhenius(mu_H_max, theta_mu_H, T) * nu_NO * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * this._monod(S_NH, K_NH) * this._monod(S_HCO, K_HCO) * this._monod(X_STO/X_H, K_STO) * X_H; rates[4] = X_H == 0 ? 0 : this._arrhenius(mu_H_max, theta_mu_H, T) * nu_NO * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * this._monod(S_NH, K_NH) * this._monod(S_HCO, K_HCO) * this._monod(X_STO/X_H, K_STO) * X_H;
rates[5] = this._arrhenius(b_H_O, theta_b_H_O, T) * this._monod(S_O, K_O) * X_H; rates[5] = this._arrhenius(b_H_O, theta_b_H_O, T) * this._monod(S_O, K_O) * X_H;
rates[6] = this._arrhenius(b_H_NO, theta_b_H_NO, T) * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * X_H; rates[6] = this._arrhenius(b_H_NO, theta_b_H_NO, T) * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * X_H;
rates[7] = this._arrhenius(b_STO_O, theta_b_STO_O, T) * this._monod(S_O, K_O) * X_H; rates[7] = this._arrhenius(b_STO_O, theta_b_STO_O, T) * this._monod(S_O, K_O) * X_H;
rates[8] = this._arrhenius(b_STO_NO, theta_b_STO_NO, T) * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * X_STO; rates[8] = this._arrhenius(b_STO_NO, theta_b_STO_NO, T) * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * X_STO;
// Autotrophs // Autotrophs
rates[9] = this._arrhenius(mu_A_max, theta_mu_A, T) * this._monod(S_O, K_A_O) * this._monod(S_NH, K_A_NH) * this._monod(S_HCO, K_A_HCO) * X_A; rates[9] = this._arrhenius(mu_A_max, theta_mu_A, T) * this._monod(S_O, K_A_O) * this._monod(S_NH, K_A_NH) * this._monod(S_HCO, K_A_HCO) * X_A;
rates[10] = this._arrhenius(b_A_O, theta_b_A_O, T) * this._monod(S_O, K_O) * X_A; rates[10] = this._arrhenius(b_A_O, theta_b_A_O, T) * this._monod(S_O, K_O) * X_A;
rates[11] = this._arrhenius(b_A_NO, theta_b_A_NO, T) * this._inv_monod(S_O, K_A_O) * this._monod(S_NO, K_NO) * X_A; rates[11] = this._arrhenius(b_A_NO, theta_b_A_NO, T) * this._inv_monod(S_O, K_A_O) * this._monod(S_NO, K_NO) * X_A;
return rates; return rates;
} }
/** /**
* Computes the change in concentrations of reaction species based on the current state and temperature. * Computes the change in concentrations of reaction species based on the current state and temperature.
* @param {Array} state - State vector containing concentrations of reaction species. * @param {Array} state - State vector containing concentrations of reaction species.
* @param {number} [T=20] - Temperature in degrees Celsius (default is 20). * @param {number} [T=20] - Temperature in degrees Celsius (default is 20).
* @returns {Array} - Change in reaction species concentrations. * @returns {Array} - Change in reaction species concentrations.
*/ */
compute_dC(state, T = 20) { // compute changes in concentrations compute_dC(state, T = 20) { // compute changes in concentrations
// state: S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS // state: S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS
return math.multiply(this.stoi_matrix, this.compute_rates(state, T)); return math.multiply(this.stoi_matrix, this.compute_rates(state, T));
} }
} }
module.exports = ASM3; module.exports = ASM3;

884
src/specificClass.js
View File

@@ -1,482 +1,420 @@
const ASM3 = require('./reaction_modules/asm3_class.js'); const ASM3 = require('./reaction_modules/asm3_class.js');
const { create, all, isArray } = require('mathjs'); const { create, all, isArray } = require('mathjs');
const { assertNoNaN } = require('./utils.js'); const { assertNoNaN } = require('./utils.js');
const { childRegistrationUtils, logger, MeasurementContainer } = require('generalFunctions'); const { childRegistrationUtils, logger, MeasurementContainer } = require('generalFunctions');
const EventEmitter = require('events'); const EventEmitter = require('events');
const mathConfig = { const mathConfig = {
matrix: 'Array' // use Array as the matrix type matrix: 'Array' // use Array as the matrix type
}; };
const math = create(all, mathConfig); const math = create(all, mathConfig);
const S_O_INDEX = 0; const S_O_INDEX = 0;
const NUM_SPECIES = 13; const NUM_SPECIES = 13;
const DEBUG = false; const BC_PADDING = 2;
const DEBUG = false;
class Reactor {
/** class Reactor {
* Reactor base class. /**
* @param {object} config - Configuration object containing reactor parameters. * Reactor base class.
*/ * @param {object} config - Configuration object containing reactor parameters.
constructor(config) { */
this.config = config; constructor(config) {
// EVOLV stuff this.config = config;
this.logger = new logger(this.config.general.logging.enabled, this.config.general.logging.logLevel, config.general.name); // EVOLV stuff
this.emitter = new EventEmitter(); this.logger = new logger(this.config.general.logging.enabled, this.config.general.logging.logLevel, config.general.name);
this.measurements = new MeasurementContainer(); this.emitter = new EventEmitter();
this.upstreamReactor = null; this.measurements = new MeasurementContainer();
this.childRegistrationUtils = new childRegistrationUtils(this); // Child registration utility this.upstreamReactor = null;
this.childRegistrationUtils = new childRegistrationUtils(this); // Child registration utility
this.asm = new ASM3(); this.parent = []; // Gets assigned via child registration
this.volume = config.volume; // fluid volume reactor [m3] this.upstreamReactor = null;
this.downstreamReactor = null;
this.Fs = Array(config.n_inlets).fill(0); // fluid debits per inlet [m3 d-1]
this.Cs_in = Array.from(Array(config.n_inlets), () => new Array(NUM_SPECIES).fill(0)); // composition influents this.asm = new ASM3();
this.OTR = 0.0; // oxygen transfer rate [g O2 d-1 m-3]
this.temperature = 20; // temperature [C] this.volume = config.volume; // fluid volume reactor [m3]
this.kla = config.kla; // if NaN, use externaly provided OTR [d-1] this.Fs = Array(config.n_inlets).fill(0); // fluid debits per inlet [m3 d-1]
this.Cs_in = Array.from(Array(config.n_inlets), () => new Array(NUM_SPECIES).fill(0)); // composition influents
this.currentTime = Date.now(); // milliseconds since epoch [ms] this.OTR = 0.0; // oxygen transfer rate [g O2 d-1 m-3]
this.timeStep = 1 / (24*60*60) * this.config.timeStep; // time step in seconds, converted to days. this.temperature = 20; // temperature [C]
this.speedUpFactor = config.speedUpFactor ?? 1; // speed up factor for simulation
} this.kla = config.kla; // if NaN, use externaly provided OTR [d-1]
/** this.currentTime = Date.now(); // milliseconds since epoch [ms]
* Setter for influent data. this.timeStep = 1 / (24*60*60) * this.config.timeStep; // time step in seconds, converted to days.
* @param {object} input - Input object (msg) containing payload with inlet index, flow rate, and concentrations. this.speedUpFactor = 100; // speed up factor for simulation, 60 means 1 minute per simulated second
*/ }
set setInfluent(input) {
let index_in = input.payload.inlet; /**
this.Fs[index_in] = input.payload.F; * Setter for influent data.
this.Cs_in[index_in] = input.payload.C; * @param {object} input - Input object (msg) containing payload with inlet index, flow rate, and concentrations.
} */
set setInfluent(input) {
/** let index_in = input.payload.inlet;
* Setter for OTR (Oxygen Transfer Rate). this.Fs[index_in] = input.payload.F;
* @param {object} input - Input object (msg) containing payload with OTR value [g O2 d-1 m-3]. this.Cs_in[index_in] = input.payload.C;
*/ }
set setOTR(input) {
this.OTR = input.payload; /**
} * Setter for OTR (Oxygen Transfer Rate).
* @param {object} input - Input object (msg) containing payload with OTR value [g O2 d-1 m-3].
/** */
* Setter for reactor temperature [C]. set setOTR(input) {
* Accepts either a direct numeric payload or { value } object payload. this.OTR = input.payload;
* @param {object} input - Input object (msg) }
*/
set setTemperature(input) { /**
const payload = input?.payload; * Getter for effluent data.
const rawValue = (payload && typeof payload === 'object' && payload.value !== undefined) * @returns {object} Effluent data object (msg), defaults to inlet 0.
? payload.value */
: payload; get getEffluent() { // getter for Effluent, defaults to inlet 0
const parsedValue = Number(rawValue); if (isArray(this.state.at(-1))) {
if (!Number.isFinite(parsedValue)) { return { topic: "Fluent", payload: { inlet: 0, F: math.sum(this.Fs), C: this.state.at(-1) }, timestamp: this.currentTime };
this.logger.warn(`Invalid temperature input: ${rawValue}`); }
return; return { topic: "Fluent", payload: { inlet: 0, F: math.sum(this.Fs), C: this.state }, timestamp: this.currentTime };
} }
this.temperature = parsedValue;
} /**
* Calculate the oxygen transfer rate (OTR) based on the dissolved oxygen concentration and temperature.
/** * @param {number} S_O - Dissolved oxygen concentration [g O2 m-3].
* Getter for effluent data. * @param {number} T - Temperature in Celsius, default to 20 C.
* @returns {object} Effluent data object (msg), defaults to inlet 0. * @returns {number} - Calculated OTR [g O2 d-1 m-3].
*/ */
get getEffluent() { // getter for Effluent, defaults to inlet 0
if (isArray(this.state.at(-1))) {
return { topic: "Fluent", payload: { inlet: 0, F: math.sum(this.Fs), C: this.state.at(-1) }, timestamp: this.currentTime };
}
return { topic: "Fluent", payload: { inlet: 0, F: math.sum(this.Fs), C: this.state }, timestamp: this.currentTime };
}
get getGridProfile() { return null; }
/**
* Calculate the oxygen transfer rate (OTR) based on the dissolved oxygen concentration and temperature.
* @param {number} S_O - Dissolved oxygen concentration [g O2 m-3].
* @param {number} T - Temperature in Celsius, default to 20 C.
* @returns {number} - Calculated OTR [g O2 d-1 m-3].
*/
_calcOTR(S_O, T = 20.0) { // caculate the OTR using basic correlation, default to temperature: 20 C _calcOTR(S_O, T = 20.0) { // caculate the OTR using basic correlation, default to temperature: 20 C
let S_O_sat = 14.652 - 4.1022e-1 * T + 7.9910e-3 * T*T + 7.7774e-5 * T*T*T; let S_O_sat = 14.652 - 4.1022e-1 * T + 7.9910e-3 * T*T + 7.7774e-5 * T*T*T;
return this.kla * (S_O_sat - S_O); return this.kla * (S_O_sat - S_O);
} }
_calcOxygenSaturation(T = 20.0) { /**
return 14.652 - 4.1022e-1 * T + 7.9910e-3 * T*T + 7.7774e-5 * T*T*T; * Clip values in an array to zero.
} * @param {Array} arr - Array of values to clip.
* @returns {Array} - New array with values clipped to zero.
_capDissolvedOxygen(state) { */
const saturation = this._calcOxygenSaturation(this.temperature); _arrayClip2Zero(arr) {
const capRow = (row) => { if (Array.isArray(arr)) {
if (!Array.isArray(row)) { return arr.map(x => this._arrayClip2Zero(x));
return row; } else {
} return arr < 0 ? 0 : arr;
const next = row.slice();
if (Number.isFinite(next[S_O_INDEX])) {
next[S_O_INDEX] = Math.max(0, Math.min(next[S_O_INDEX], saturation));
}
return next;
};
if (Array.isArray(state) && Array.isArray(state[0])) {
return state.map(capRow);
} }
return capRow(state);
} }
/** registerChild(child, softwareType) {
* Clip values in an array to zero. switch (softwareType) {
* @param {Array} arr - Array of values to clip. case "measurement":
* @returns {Array} - New array with values clipped to zero. this.logger.debug(`Registering measurement child.`);
*/ this._connectMeasurement(child);
_arrayClip2Zero(arr) { break;
if (Array.isArray(arr)) { case "reactor":
return arr.map(x => this._arrayClip2Zero(x)); this.logger.debug(`Registering reactor child.`);
} else { this._connectReactor(child);
return arr < 0 ? 0 : arr; break;
}
} default:
this.logger.error(`Unrecognized softwareType: ${softwareType}`);
registerChild(child, softwareType) { }
switch (softwareType) { }
case "measurement":
this.logger.debug(`Registering measurement child.`); _connectMeasurement(measurementChild) {
this._connectMeasurement(child); if (!measurementChild) {
break; this.logger.warn("Invalid measurement provided.");
case "reactor": return;
this.logger.debug(`Registering reactor child.`); }
this._connectReactor(child);
break; const position = measurementChild.config.functionality.positionVsParent;
const measurementType = measurementChild.config.asset.type;
default: const eventName = `${measurementType}.measured.${position}`;
this.logger.error(`Unrecognized softwareType: ${softwareType}`);
} // Register event listener for measurement updates
} measurementChild.measurements.emitter.on(eventName, (eventData) => {
this.logger.debug(`${position} ${measurementType} from ${eventData.childName}: ${eventData.value} ${eventData.unit}`);
_connectMeasurement(measurement) {
if (!measurement) { // Store directly in parent's measurement container
this.logger.warn("Invalid measurement provided."); this.measurements
return; .type(measurementType)
} .variant("measured")
.position(position)
let position; .value(eventData.value, eventData.timestamp, eventData.unit);
if (measurement.config.functionality.distance !== 'undefined') {
position = measurement.config.functionality.distance; this._updateMeasurement(measurementType, eventData.value, position, eventData);
} else { });
position = measurement.config.functionality.positionVsParent; }
}
const measurementType = measurement.config.asset.type;
const key = `${measurementType}_${position}`; _connectReactor(reactorChild) {
const eventName = `${measurementType}.measured.${position}`; if (!reactorChild) {
this.logger.warn("Invalid reactor provided.");
// Register event listener for measurement updates return;
measurement.measurements.emitter.on(eventName, (eventData) => { }
this.logger.debug(`${position} ${measurementType} from ${eventData.childName}: ${eventData.value} ${eventData.unit}`);
this.upstreamReactor = reactorChild;
// Store directly in parent's measurement container reactorChild.downstreamReactor = this;
this.measurements
.type(measurementType) reactorChild.emitter.on("stateChange", (data) => {
.variant("measured") this.logger.debug(`State change of upstream reactor detected.`);
.position(position) this.updateState(data);
.value(eventData.value, eventData.timestamp, eventData.unit); });
}
this._updateMeasurement(measurementType, eventData.value, position, eventData);
});
} _updateMeasurement(measurementType, value, position, context) {
this.logger.debug(`---------------------- updating ${measurementType} ------------------ `);
switch (measurementType) {
_connectReactor(reactor) { case "temperature":
if (!reactor) { if (position == "atEquipment") {
this.logger.warn("Invalid reactor provided."); this.temperature = value;
return; }
} break;
default:
this.upstreamReactor = reactor; this.logger.error(`Type '${measurementType}' not recognized for measured update.`);
return;
reactor.emitter.on("stateChange", (data) => { }
this.logger.debug(`State change of upstream reactor detected.`); }
this.updateState(data);
}); /**
} * Update the reactor state based on the new time.
* @param {number} newTime - New time to update reactor state to, in milliseconds since epoch.
*/
_updateMeasurement(measurementType, value, position, context) { updateState(newTime = Date.now()) { // expect update with timestamp
this.logger.debug(`---------------------- updating ${measurementType} ------------------ `); const day2ms = 1000 * 60 * 60 * 24;
switch (measurementType) {
case "temperature": if (this.upstreamReactor) {
if (position == "atEquipment") { this.setInfluent = this.upstreamReactor.getEffluent;
this.temperature = value; }
}
break; let n_iter = Math.floor(this.speedUpFactor * (newTime-this.currentTime) / (this.timeStep*day2ms));
default: if (n_iter) {
this.logger.error(`Type '${measurementType}' not recognized for measured update.`); let n = 0;
return; while (n < n_iter) {
} this.tick(this.timeStep);
} n += 1;
}
/** this.currentTime += n_iter * this.timeStep * day2ms / this.speedUpFactor;
* Update the reactor state based on the new time. this.emitter.emit("stateChange", this.currentTime);
* @param {number} newTime - New time to update reactor state to, in milliseconds since epoch. }
*/ }
updateState(newTime = Date.now()) { // expect update with timestamp }
const day2ms = 1000 * 60 * 60 * 24;
class Reactor_CSTR extends Reactor {
if (this.upstreamReactor) { /**
this.setInfluent = this.upstreamReactor.getEffluent; * Reactor_CSTR class for Continuous Stirred Tank Reactor.
} * @param {object} config - Configuration object containing reactor parameters.
*/
let n_iter = Math.floor(this.speedUpFactor * (newTime-this.currentTime) / (this.timeStep*day2ms)); constructor(config) {
if (n_iter) { super(config);
let n = 0; this.state = config.initialState;
while (n < n_iter) { }
this.tick(this.timeStep);
n += 1; /**
} * Tick the reactor state using the forward Euler method.
this.currentTime += n_iter * this.timeStep * day2ms / this.speedUpFactor; * @param {number} time_step - Time step for the simulation [d].
this.emitter.emit("stateChange", this.currentTime); * @returns {Array} - New reactor state.
} */
} tick(time_step) { // tick reactor state using forward Euler method
} const inflow = math.multiply(math.divide([this.Fs], this.volume), this.Cs_in)[0];
const outflow = math.multiply(-1 * math.sum(this.Fs) / this.volume, this.state);
class Reactor_CSTR extends Reactor { const reaction = this.asm.compute_dC(this.state, this.temperature);
/** const transfer = Array(NUM_SPECIES).fill(0.0);
* Reactor_CSTR class for Continuous Stirred Tank Reactor. transfer[S_O_INDEX] = isNaN(this.kla) ? this.OTR : this._calcOTR(this.state[S_O_INDEX], this.temperature); // calculate OTR if kla is not NaN, otherwise use externaly calculated OTR
* @param {object} config - Configuration object containing reactor parameters.
*/ const dC_total = math.multiply(math.add(inflow, outflow, reaction, transfer), time_step)
constructor(config) { this.state = this._arrayClip2Zero(math.add(this.state, dC_total)); // clip value element-wise to avoid negative concentrations
super(config); if(DEBUG){
this.state = config.initialState; assertNoNaN(dC_total, "change in state");
} assertNoNaN(this.state, "new state");
}
/** return this.state;
* Tick the reactor state using the forward Euler method. }
* @param {number} time_step - Time step for the simulation [d]. }
* @returns {Array} - New reactor state.
*/ class Reactor_PFR extends Reactor {
tick(time_step) { // tick reactor state using forward Euler method /**
const inflow = math.multiply(math.divide([this.Fs], this.volume), this.Cs_in)[0]; * Reactor_PFR class for Plug Flow Reactor.
const outflow = math.multiply(-1 * math.sum(this.Fs) / this.volume, this.state); * @param {object} config - Configuration object containing reactor parameters.
const reaction = this.asm.compute_dC(this.state, this.temperature); */
const transfer = Array(NUM_SPECIES).fill(0.0); constructor(config) {
transfer[S_O_INDEX] = isNaN(this.kla) ? this.OTR : this._calcOTR(this.state[S_O_INDEX], this.temperature); // calculate OTR if kla is not NaN, otherwise use externaly calculated OTR super(config);
const dC_total = math.multiply(math.add(inflow, outflow, reaction, transfer), time_step) this.length = config.length; // reactor length [m]
this.state = this._capDissolvedOxygen(this._arrayClip2Zero(math.add(this.state, dC_total))); // clip concentrations and enforce physical DO saturation this.n_x = config.resolution_L; // number of slices
if(DEBUG){
assertNoNaN(dC_total, "change in state"); this.d_x = this.length / this.n_x;
assertNoNaN(this.state, "new state"); this.A = this.volume / this.length; // crosssectional area [m2]
}
return this.state; this.alpha = config.alpha;
}
} this.state = Array.from(Array(this.n_x), () => config.initialState.slice());
this.extendedState = Array.from(Array(this.n_x + 2*BC_PADDING), () => new Array(NUM_SPECIES).fill(0));
class Reactor_PFR extends Reactor {
/** // initialise extended state
* Reactor_PFR class for Plug Flow Reactor. this.state.forEach((row, i) => this.extendedState[i+BC_PADDING] = row);
* @param {object} config - Configuration object containing reactor parameters.
*/ this.D = 0.0; // axial dispersion [m2 d-1]
constructor(config) {
super(config); this.D_op = this._makeDoperator();
assertNoNaN(this.D_op, "Derivative operator");
this.length = config.length; // reactor length [m]
this.n_x = config.resolution_L; // number of slices this.D2_op = this._makeD2operator();
assertNoNaN(this.D2_op, "Second derivative operator");
this.d_x = this.length / this.n_x; }
this.A = this.volume / this.length; // crosssectional area [m2]
/**
this.alpha = config.alpha; * Setter for axial dispersion.
* @param {object} input - Input object (msg) containing payload with dispersion value [m2 d-1].
this.state = Array.from(Array(this.n_x), () => config.initialState.slice()) */
set setDispersion(input) {
this.D = 0.0; // axial dispersion [m2 d-1] this.D = input.payload;
}
this.D_op = this._makeDoperator(true, true);
assertNoNaN(this.D_op, "Derivative operator"); updateState(newTime) {
super.updateState(newTime);
this.D2_op = this._makeD2operator(); let Pe_local = this.d_x*math.sum(this.Fs)/(this.D*this.A)
assertNoNaN(this.D2_op, "Second derivative operator"); let Co_D = this.D*this.timeStep/(this.d_x*this.d_x);
}
(Pe_local >= 2) && this.logger.warn(`Local Péclet number (${Pe_local}) is too high! Increase reactor resolution.`);
get getGridProfile() { (Co_D >= 0.5) && this.logger.warn(`Courant number (${Co_D}) is too high! Reduce time step size.`);
return {
grid: this.state.map(row => row.slice()), if(DEBUG) {
n_x: this.n_x, console.log("Inlet state max " + math.max(this.state[0]))
d_x: this.d_x, console.log("Pe total " + this.length*math.sum(this.Fs)/(this.D*this.A));
length: this.length, console.log("Pe local " + Pe_local);
species: ['S_O','S_I','S_S','S_NH','S_N2','S_NO','S_HCO', console.log("Co ad " + math.sum(this.Fs)*this.timeStep/(this.A*this.d_x));
'X_I','X_S','X_H','X_STO','X_A','X_TS'], console.log("Co D " + Co_D);
timestamp: this.currentTime }
}; }
}
/**
/** * Tick the reactor state using explicit finite difference method.
* Setter for axial dispersion. * @param {number} time_step - Time step for the simulation [d].
* @param {object} input - Input object (msg) containing payload with dispersion value [m2 d-1]. * @returns {Array} - New reactor state.
*/ */
set setDispersion(input) { tick(time_step) {
this.D = input.payload; this._applyBoundaryConditions();
}
const dispersion = math.multiply(this.D / (this.d_x*this.d_x), this.D2_op, this.extendedState);
updateState(newTime) { const advection = math.multiply(-1 * math.sum(this.Fs) / (this.A*this.d_x), this.D_op, this.extendedState);
super.updateState(newTime); const reaction = this.extendedState.map((state_slice) => this.asm.compute_dC(state_slice, this.temperature));
let Pe_local = this.d_x*math.sum(this.Fs)/(this.D*this.A) const transfer = Array.from(Array(this.n_x+2*BC_PADDING), () => new Array(NUM_SPECIES).fill(0));
let Co_D = this.D*this.timeStep/(this.d_x*this.d_x);
if (isNaN(this.kla)) { // calculate OTR if kla is not NaN, otherwise use externally calculated OTR
(Pe_local >= 2) && this.logger.warn(`Local Péclet number (${Pe_local}) is too high! Increase reactor resolution.`); for (let i = BC_PADDING+1; i < BC_PADDING+this.n_x - 1; i++) {
(Co_D >= 0.5) && this.logger.warn(`Courant number (${Co_D}) is too high! Reduce time step size.`); transfer[i][S_O_INDEX] = this.OTR * this.n_x/(this.n_x-2);
}
if(DEBUG) { } else {
console.log("Inlet state max " + math.max(this.state[0])) for (let i = BC_PADDING+1; i < BC_PADDING+this.n_x - 1; i++) {
console.log("Pe total " + this.length*math.sum(this.Fs)/(this.D*this.A)); transfer[i][S_O_INDEX] = this._calcOTR(this.extendedState[i][S_O_INDEX], this.temperature) * this.n_x/(this.n_x-2);
console.log("Pe local " + Pe_local); }
console.log("Co ad " + math.sum(this.Fs)*this.timeStep/(this.A*this.d_x)); }
console.log("Co D " + Co_D);
} const dC_total = math.multiply(math.add(dispersion, advection, reaction, transfer).slice(BC_PADDING, this.n_x+BC_PADDING), time_step);
}
const stateNew = math.add(this.state, dC_total);
/**
* Tick the reactor state using explicit finite difference method. if (DEBUG) {
* @param {number} time_step - Time step for the simulation [d]. assertNoNaN(dispersion, "dispersion");
* @returns {Array} - New reactor state. assertNoNaN(advection, "advection");
*/ assertNoNaN(reaction, "reaction");
tick(time_step) { assertNoNaN(dC_total, "change in state");
const dispersion = math.multiply(this.D / (this.d_x*this.d_x), this.D2_op, this.state); assertNoNaN(stateNew, "new state post BC");
const advection = math.multiply(-1 * math.sum(this.Fs) / (this.A*this.d_x), this.D_op, this.state); }
const reaction = this.state.map((state_slice) => this.asm.compute_dC(state_slice, this.temperature));
const transfer = Array.from(Array(this.n_x), () => new Array(NUM_SPECIES).fill(0)); this.state = this._arrayClip2Zero(stateNew);
this.state.forEach((row, i) => this.extendedState[i+BC_PADDING] = row);
if (isNaN(this.kla)) { // calculate OTR if kla is not NaN, otherwise use externally calculated OTR
for (let i = 1; i < this.n_x - 1; i++) {
transfer[i][S_O_INDEX] = this.OTR * this.n_x/(this.n_x-2);
}
} else {
for (let i = 1; i < this.n_x - 1; i++) {
transfer[i][S_O_INDEX] = this._calcOTR(this.state[i][S_O_INDEX], this.temperature) * this.n_x/(this.n_x-2);
}
}
const dC_total = math.multiply(math.add(dispersion, advection, reaction, transfer), time_step);
const stateNew = math.add(this.state, dC_total);
this._applyBoundaryConditions(stateNew);
if (DEBUG) {
assertNoNaN(dispersion, "dispersion");
assertNoNaN(advection, "advection");
assertNoNaN(reaction, "reaction");
assertNoNaN(dC_total, "change in state");
assertNoNaN(stateNew, "new state post BC");
}
this.state = this._capDissolvedOxygen(this._arrayClip2Zero(stateNew));
return stateNew; return stateNew;
} }
_updateMeasurement(measurementType, value, position, context) { _updateMeasurement(measurementType, value, position, context) {
switch(measurementType) { switch(measurementType) {
case "quantity (oxygen)": case "quantity (oxygen)":
if (!Number.isFinite(position) || !Number.isFinite(value) || this.config.length <= 0) { let grid_pos = Math.round(context.distance / this.config.length * this.n_x);
this.logger.warn(`Ignoring oxygen measurement update with invalid data (position=${position}, value=${value}).`); this.state[grid_pos][S_O_INDEX] = value; // naive approach for reconciling measurements and simulation
break; break;
} default:
{ super._updateMeasurement(measurementType, value, position, context);
// Clamp sensor-derived position to valid PFR grid bounds. }
const rawIndex = Math.round(position / this.config.length * this.n_x); }
const grid_pos = Math.max(0, Math.min(this.n_x - 1, rawIndex));
this.state[grid_pos][S_O_INDEX] = value; // reconcile measured oxygen concentration into nearest grid cell /**
} * Apply boundary conditions to the reactor state.
break; * for inlet, apply generalised Danckwerts BC, if there is not flow, apply Neumann BC with no flux
default: * for outlet, apply regular Danckwerts BC (Neumann BC with no flux)
super._updateMeasurement(measurementType, value, position, context); */
} _applyBoundaryConditions() {
} if (this.upstreamReactor) {
for (let i = 0; i < BC_PADDING; i++) {
/** this.extendedState[i] = this.upstreamReactor.state.at(i-BC_PADDING);
* Apply boundary conditions to the reactor state. }
* for inlet, apply generalised Danckwerts BC, if there is not flow, apply Neumann BC with no flux } else {
* for outlet, apply regular Danckwerts BC (Neumann BC with no flux) if (math.sum(this.Fs) > 0) { // Danckwerts BC
* @param {Array} state - Current reactor state without enforced BCs. const BC_C_in = math.multiply(1 / math.sum(this.Fs), [this.Fs], this.Cs_in)[0];
*/ const BC_dispersion_term = (1-this.alpha)*this.D*this.A/(math.sum(this.Fs)*this.d_x);
_applyBoundaryConditions(state) { this.extendedState[BC_PADDING] = math.multiply(1/(1+BC_dispersion_term), math.add(BC_C_in, math.multiply(BC_dispersion_term, this.extendedState[BC_PADDING+1])));
if (math.sum(this.Fs) > 0) { // Danckwerts BC this.extendedState[BC_PADDING-1] = math.add(math.multiply(2, this.extendedState[BC_PADDING]), math.multiply(-2, this.extendedState[BC_PADDING+2]), this.extendedState[BC_PADDING+3]);
const BC_C_in = math.multiply(1 / math.sum(this.Fs), [this.Fs], this.Cs_in)[0]; } else {
const BC_dispersion_term = (1-this.alpha)*this.D*this.A/(math.sum(this.Fs)*this.d_x); for (let i = 0; i < BC_PADDING; i++) {
state[0] = math.multiply(1/(1+BC_dispersion_term), math.add(BC_C_in, math.multiply(BC_dispersion_term, state[1]))); this.extendedState[i] = this.extendedState[BC_PADDING];
} else { }
state[0] = state[1]; }
} }
// Neumann BC (no flux)
state[this.n_x-1] = state[this.n_x-2]; if (this.downstreamReactor) {
} for (let i = 0; i < BC_PADDING; i++) {
this.extendedState[this.n_x+BC_PADDING+i] = this.downstreamReactor.state[i];
/** }
* Create finite difference first derivative operator. } else {
* @param {boolean} central - Use central difference scheme if true, otherwise use upwind scheme. // Neumann BC (no flux)
* @param {boolean} higher_order - Use higher order scheme if true, otherwise use first order scheme. for (let i = 0; i < BC_PADDING; i++) {
* @returns {Array} - First derivative operator matrix. this.extendedState[BC_PADDING+this.n_x+i] = this.extendedState.at(-1-BC_PADDING);
*/ }
_makeDoperator(central = false, higher_order = false) { // create gradient operator }
if (higher_order) { }
if (central) {
const I = math.resize(math.diag(Array(this.n_x).fill(1/12), -2), [this.n_x, this.n_x]); /**
const A = math.resize(math.diag(Array(this.n_x).fill(-2/3), -1), [this.n_x, this.n_x]); * Create finite difference first derivative operator.
const B = math.resize(math.diag(Array(this.n_x).fill(2/3), 1), [this.n_x, this.n_x]); * @returns {Array} - First derivative operator matrix.
const C = math.resize(math.diag(Array(this.n_x).fill(-1/12), 2), [this.n_x, this.n_x]); */
const D = math.add(I, A, B, C); _makeDoperator() { // create gradient operator
const NearBoundary = Array(this.n_x).fill(0.0); const D_size = this.n_x+2*BC_PADDING;
NearBoundary[0] = -1/4; const I = math.resize(math.diag(Array(D_size).fill(1/12), -2), [D_size, D_size]);
NearBoundary[1] = -5/6; const A = math.resize(math.diag(Array(D_size).fill(-2/3), -1), [D_size, D_size]);
NearBoundary[2] = 3/2; const B = math.resize(math.diag(Array(D_size).fill(2/3), 1), [D_size, D_size]);
NearBoundary[3] = -1/2; const C = math.resize(math.diag(Array(D_size).fill(-1/12), 2), [D_size, D_size]);
NearBoundary[4] = 1/12; const D = math.add(I, A, B, C);
D[1] = NearBoundary; // set by BCs elsewhere
NearBoundary.reverse(); D.forEach((row, i) => i < BC_PADDING || i >= this.n_x+BC_PADDING ? row.fill(0) : row);
D[this.n_x-2] = math.multiply(-1, NearBoundary); return D;
D[0] = Array(this.n_x).fill(0); // set by BCs elsewhere }
D[this.n_x-1] = Array(this.n_x).fill(0);
return D; /**
} else { * Create central finite difference second derivative operator.
throw new Error("Upwind higher order method not implemented! Use central scheme instead."); * @returns {Array} - Second derivative operator matrix.
} */
} else { _makeD2operator() { // create the central second derivative operator
const I = math.resize(math.diag(Array(this.n_x).fill(1 / (1+central)), central), [this.n_x, this.n_x]); const D_size = this.n_x+2*BC_PADDING;
const A = math.resize(math.diag(Array(this.n_x).fill(-1 / (1+central)), -1), [this.n_x, this.n_x]); const I = math.diag(Array(D_size).fill(-2), 0);
const D = math.add(I, A); const A = math.resize(math.diag(Array(D_size).fill(1), 1), [D_size, D_size]);
D[0] = Array(this.n_x).fill(0); // set by BCs elsewhere const B = math.resize(math.diag(Array(D_size).fill(1), -1), [D_size, D_size]);
D[this.n_x-1] = Array(this.n_x).fill(0); const D2 = math.add(I, A, B);
return D; // set by BCs elsewhere
} D2.forEach((row, i) => i < BC_PADDING || i >= this.n_x+BC_PADDING ? row.fill(0) : row);
} return D2;
}
/** }
* Create central finite difference second derivative operator.
* @returns {Array} - Second derivative operator matrix. module.exports = { Reactor_CSTR, Reactor_PFR };
*/
_makeD2operator() { // create the central second derivative operator // DEBUG
const I = math.diag(Array(this.n_x).fill(-2), 0); // state: S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS
const A = math.resize(math.diag(Array(this.n_x).fill(1), 1), [this.n_x, this.n_x]); // let initial_state = [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1];
const B = math.resize(math.diag(Array(this.n_x).fill(1), -1), [this.n_x, this.n_x]); // const Reactor = new Reactor_PFR(200, 10, 10, 1, 100, initial_state);
const D2 = math.add(I, A, B); // Reactor.Cs_in[0] = [0.0, 30., 100., 16., 0., 0., 5., 25., 75., 30., 0., 0., 125.];
D2[0] = Array(this.n_x).fill(0); // set by BCs elsewhere // Reactor.Fs[0] = 10;
D2[this.n_x - 1] = Array(this.n_x).fill(0); // Reactor.D = 0.01;
return D2; // let N = 0;
} // while (N < 5000) {
} // console.log(Reactor.tick(0.001));
// N += 1;
module.exports = { Reactor_CSTR, Reactor_PFR }; // }
// DEBUG
// state: S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS
// let initial_state = [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1];
// const Reactor = new Reactor_PFR(200, 10, 10, 1, 100, initial_state);
// Reactor.Cs_in[0] = [0.0, 30., 100., 16., 0., 0., 5., 25., 75., 30., 0., 0., 125.];
// Reactor.Fs[0] = 10;
// Reactor.D = 0.01;
// let N = 0;
// while (N < 5000) {
// console.log(Reactor.tick(0.001));
// N += 1;
// }

34
src/utils.js
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/** /**
* Assert that no NaN values are present in an array. * Assert that no NaN values are present in an array.
* @param {Array} arr * @param {Array} arr
* @param {string} label * @param {string} label
*/ */
function assertNoNaN(arr, label = "array") { function assertNoNaN(arr, label = "array") {
if (Array.isArray(arr)) { if (Array.isArray(arr)) {
for (const el of arr) { for (const el of arr) {
assertNoNaN(el, label); assertNoNaN(el, label);
} }
} else { } else {
if (Number.isNaN(arr)) { if (Number.isNaN(arr)) {
throw new Error(`NaN detected in ${label}!`); throw new Error(`NaN detected in ${label}!`);
} }
} }
} }
module.exports = { assertNoNaN }; module.exports = { assertNoNaN };

12
test/README.md
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# reactor Test Suite Layout
Required EVOLV layout:
- basic/
- integration/
- edge/
- helpers/
Baseline structure tests:
- basic/structure-module-load.basic.test.js
- integration/structure-examples.integration.test.js
- edge/structure-examples-node-type.edge.test.js

0
test/basic/.gitkeep
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55
test/basic/constructor.basic.test.js
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const test = require('node:test');
const assert = require('node:assert/strict');
const NodeClass = require('../../src/nodeClass');
const { Reactor_CSTR, Reactor_PFR } = require('../../src/specificClass');
const { makeUiConfig, makeReactorConfig, makeNodeStub } = require('../helpers/factories');
test('_loadConfig coerces numeric fields and builds initial state vector', () => {
const inst = Object.create(NodeClass.prototype);
inst.node = { id: 'n-reactor-1' };
inst.name = 'reactor';
inst._loadConfig(
makeUiConfig({
volume: '12.5',
length: '9',
resolution_L: '7',
alpha: '0.5',
n_inlets: '3',
timeStep: '2',
S_O_init: '1.1',
}),
);
assert.equal(inst.config.volume, 12.5);
assert.equal(inst.config.length, 9);
assert.equal(inst.config.resolution_L, 7);
assert.equal(inst.config.alpha, 0.5);
assert.equal(inst.config.n_inlets, 3);
assert.equal(inst.config.timeStep, 2);
assert.equal(inst.config.initialState.length, 13);
assert.equal(inst.config.initialState[0], 1.1);
});
test('_setupClass selects Reactor_CSTR when configured as CSTR', () => {
const inst = Object.create(NodeClass.prototype);
inst.node = makeNodeStub();
inst.config = makeReactorConfig({ reactor_type: 'CSTR' });
inst._setupClass();
assert.ok(inst.source instanceof Reactor_CSTR);
assert.equal(inst.node.source, inst.source);
});
test('_setupClass selects Reactor_PFR when configured as PFR', () => {
const inst = Object.create(NodeClass.prototype);
inst.node = makeNodeStub();
inst.config = makeReactorConfig({ reactor_type: 'PFR', length: 10, resolution_L: 5 });
inst._setupClass();
assert.ok(inst.source instanceof Reactor_PFR);
assert.equal(inst.node.source, inst.source);
});

42
test/basic/cstr-tick.basic.test.js
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const test = require('node:test');
const assert = require('node:assert/strict');
const { Reactor_CSTR } = require('../../src/specificClass');
const { makeReactorConfig } = require('../helpers/factories');
const NUM_SPECIES = 13;
test('Reactor_CSTR tick clips negative concentrations to zero', () => {
const reactor = new Reactor_CSTR(
makeReactorConfig({
reactor_type: 'CSTR',
volume: 1,
n_inlets: 1,
kla: NaN,
S_O_init: 0.1,
S_I_init: 0.1,
S_S_init: 0.1,
S_NH_init: 0.1,
S_N2_init: 0.1,
S_NO_init: 0.1,
S_HCO_init: 0.1,
X_I_init: 0.1,
X_S_init: 0.1,
X_H_init: 0.1,
X_STO_init: 0.1,
X_A_init: 0.1,
X_TS_init: 0.1,
}),
);
reactor.asm = {
compute_dC: () => Array(NUM_SPECIES).fill(0),
};
reactor.Fs[0] = 1;
reactor.Cs_in[0] = Array(NUM_SPECIES).fill(0);
reactor.tick(1);
assert.equal(reactor.state.every((v) => Number.isFinite(v) && v >= 0), true);
assert.equal(reactor.state.every((v) => v === 0), true);
});

38
test/basic/effluent-shape.basic.test.js
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const test = require('node:test');
const assert = require('node:assert/strict');
const { Reactor_CSTR, Reactor_PFR } = require('../../src/specificClass');
const { makeReactorConfig } = require('../helpers/factories');
test('CSTR getEffluent returns flat concentration vector', () => {
const reactor = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR', n_inlets: 1 }));
reactor.state = Array.from({ length: 13 }, (_, i) => i + 1);
reactor.Fs[0] = 5;
const effluent = reactor.getEffluent;
assert.equal(effluent.topic, 'Fluent');
assert.equal(effluent.payload.inlet, 0);
assert.equal(effluent.payload.F, 5);
assert.deepEqual(effluent.payload.C, reactor.state);
});
test('PFR getEffluent returns last slice concentration vector', () => {
const reactor = new Reactor_PFR(
makeReactorConfig({ reactor_type: 'PFR', n_inlets: 1, length: 10, resolution_L: 4 }),
);
reactor.state = [
Array(13).fill(10),
Array(13).fill(20),
Array(13).fill(30),
Array(13).fill(40),
];
reactor.Fs[0] = 7;
const effluent = reactor.getEffluent;
assert.equal(effluent.topic, 'Fluent');
assert.equal(effluent.payload.F, 7);
assert.deepEqual(effluent.payload.C, Array(13).fill(40));
});

45
test/basic/grid-profile.basic.test.js
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const test = require('node:test');
const assert = require('node:assert/strict');
const { Reactor_CSTR, Reactor_PFR } = require('../../src/specificClass');
const { makeReactorConfig } = require('../helpers/factories');
test('CSTR getGridProfile returns null', () => {
const reactor = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR' }));
assert.equal(reactor.getGridProfile, null);
});
test('PFR getGridProfile returns state matrix with correct dimensions', () => {
const n_x = 8;
const length = 40;
const reactor = new Reactor_PFR(
makeReactorConfig({ reactor_type: 'PFR', resolution_L: n_x, length }),
);
const profile = reactor.getGridProfile;
assert.notEqual(profile, null);
assert.equal(profile.n_x, n_x);
assert.equal(profile.d_x, length / n_x);
assert.equal(profile.length, length);
assert.equal(profile.grid.length, n_x, 'grid should have n_x rows');
assert.equal(profile.grid[0].length, 13, 'each row should have 13 species');
assert.ok(Array.isArray(profile.species), 'species list should be an array');
assert.equal(profile.species.length, 13);
assert.equal(profile.species[3], 'S_NH');
assert.equal(typeof profile.timestamp, 'number');
});
test('PFR getGridProfile is mutation-safe', () => {
const reactor = new Reactor_PFR(
makeReactorConfig({ reactor_type: 'PFR', resolution_L: 5, length: 10 }),
);
const profile = reactor.getGridProfile;
const originalValue = reactor.state[0][3]; // S_NH at cell 0
// Mutate the returned grid
profile.grid[0][3] = 999;
// Reactor internal state should be unchanged
assert.equal(reactor.state[0][3], originalValue, 'mutating grid copy must not affect reactor state');
});

77
test/basic/input-routing.basic.test.js
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const test = require('node:test');
const assert = require('node:assert/strict');
const NodeClass = require('../../src/nodeClass');
const { makeNodeStub, makeREDStub } = require('../helpers/factories');
test('_attachInputHandler routes supported topics to source methods/setters', () => {
const inst = Object.create(NodeClass.prototype);
const node = makeNodeStub();
const calls = [];
const source = {
updateState(timestamp) {
calls.push(['clock', timestamp]);
},
childRegistrationUtils: {
registerChild(childSource, position) {
calls.push(['registerChild', childSource, position]);
},
},
};
Object.defineProperty(source, 'setInfluent', {
set(v) {
calls.push(['Fluent', v]);
},
});
Object.defineProperty(source, 'setOTR', {
set(v) {
calls.push(['OTR', v]);
},
});
Object.defineProperty(source, 'setTemperature', {
set(v) {
calls.push(['Temperature', v]);
},
});
Object.defineProperty(source, 'setDispersion', {
set(v) {
calls.push(['Dispersion', v]);
},
});
inst.node = node;
inst.RED = makeREDStub({
childA: {
source: { id: 'child-source-A' },
},
});
inst.source = source;
inst._attachInputHandler();
const onInput = node._handlers.input;
const sent = [];
let doneCount = 0;
onInput({ topic: 'clock', timestamp: 1000 }, (msg) => sent.push(msg), () => doneCount++);
onInput({ topic: 'Fluent', payload: { inlet: 0, F: 10, C: [] } }, () => {}, () => doneCount++);
onInput({ topic: 'OTR', payload: 3.5 }, () => {}, () => doneCount++);
onInput({ topic: 'Temperature', payload: 18.2 }, () => {}, () => doneCount++);
onInput({ topic: 'Dispersion', payload: 0.2 }, () => {}, () => doneCount++);
onInput({ topic: 'registerChild', payload: 'childA', positionVsParent: 'upstream' }, () => {}, () => doneCount++);
assert.equal(doneCount, 6);
assert.equal(sent.length, 1);
assert.equal(Array.isArray(sent[0]), true);
assert.deepEqual(calls[0], ['clock', 1000]);
assert.equal(calls.some((x) => x[0] === 'Fluent'), true);
assert.equal(calls.some((x) => x[0] === 'OTR'), true);
assert.equal(calls.some((x) => x[0] === 'Temperature'), true);
assert.equal(calls.some((x) => x[0] === 'Dispersion'), true);
assert.deepEqual(calls.at(-1), ['registerChild', { id: 'child-source-A' }, 'upstream']);
});

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test/basic/pfr-operators.basic.test.js
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const test = require('node:test');
const assert = require('node:assert/strict');
const { Reactor_PFR } = require('../../src/specificClass');
const { makeReactorConfig } = require('../helpers/factories');
test('Reactor_PFR derivative operators have expected dimensions and boundary rows', () => {
const reactor = new Reactor_PFR(
makeReactorConfig({
reactor_type: 'PFR',
length: 12,
resolution_L: 6,
volume: 60,
n_inlets: 1,
}),
);
assert.equal(reactor.D_op.length, reactor.n_x);
assert.equal(reactor.D2_op.length, reactor.n_x);
assert.equal(reactor.D_op.every((row) => row.length === reactor.n_x), true);
assert.equal(reactor.D2_op.every((row) => row.length === reactor.n_x), true);
assert.deepEqual(reactor.D_op[0], Array(reactor.n_x).fill(0));
assert.deepEqual(reactor.D_op[reactor.n_x - 1], Array(reactor.n_x).fill(0));
assert.deepEqual(reactor.D2_op[0], Array(reactor.n_x).fill(0));
assert.deepEqual(reactor.D2_op[reactor.n_x - 1], Array(reactor.n_x).fill(0));
});

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test/basic/register-child.basic.test.js
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const test = require('node:test');
const assert = require('node:assert/strict');
const NodeClass = require('../../src/nodeClass');
const { makeNodeStub } = require('../helpers/factories');
test('_registerChild emits delayed registration message on output 2', () => {
const inst = Object.create(NodeClass.prototype);
const node = makeNodeStub();
inst.node = node;
inst.config = {
functionality: {
positionVsParent: 'downstream',
},
};
const originalSetTimeout = global.setTimeout;
const delays = [];
global.setTimeout = (fn, ms) => {
delays.push(ms);
fn();
return 1;
};
try {
inst._registerChild();
} finally {
global.setTimeout = originalSetTimeout;
}
assert.deepEqual(delays, [100]);
assert.equal(node._sent.length, 1);
assert.equal(Array.isArray(node._sent[0]), true);
assert.equal(node._sent[0][2].topic, 'registerChild');
assert.equal(node._sent[0][2].payload, node.id);
assert.equal(node._sent[0][2].positionVsParent, 'downstream');
});

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test/basic/speedup-factor.basic.test.js
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const test = require('node:test');
const assert = require('node:assert/strict');
const { Reactor_CSTR } = require('../../src/specificClass');
const nodeClass = require('../../src/nodeClass');
const { makeReactorConfig, makeUiConfig, makeNodeStub, makeREDStub } = require('../helpers/factories');
/**
* Smoke tests for Fix 3: configurable speedUpFactor on Reactor.
*/
test('specificClass defaults speedUpFactor to 1 when not in config', () => {
const config = makeReactorConfig();
const reactor = new Reactor_CSTR(config);
assert.equal(reactor.speedUpFactor, 1, 'speedUpFactor should default to 1');
});
test('specificClass accepts speedUpFactor from config', () => {
const config = makeReactorConfig();
config.speedUpFactor = 10;
const reactor = new Reactor_CSTR(config);
assert.equal(reactor.speedUpFactor, 10, 'speedUpFactor should be read from config');
});
test('specificClass accepts speedUpFactor = 60 for accelerated simulation', () => {
const config = makeReactorConfig();
config.speedUpFactor = 60;
const reactor = new Reactor_CSTR(config);
assert.equal(reactor.speedUpFactor, 60, 'speedUpFactor=60 should be accepted');
});
test('nodeClass passes speedUpFactor from uiConfig to reactor config', () => {
const uiConfig = makeUiConfig({ speedUpFactor: 5 });
const node = makeNodeStub();
const RED = makeREDStub();
const nc = new nodeClass(uiConfig, RED, node, 'test-reactor');
assert.equal(nc.source.speedUpFactor, 5, 'nodeClass should pass speedUpFactor=5 to specificClass');
});
test('nodeClass defaults speedUpFactor to 1 when not in uiConfig', () => {
const uiConfig = makeUiConfig();
// Ensure speedUpFactor is not set
delete uiConfig.speedUpFactor;
const node = makeNodeStub();
const RED = makeREDStub();
const nc = new nodeClass(uiConfig, RED, node, 'test-reactor');
assert.equal(nc.source.speedUpFactor, 1, 'nodeClass should default speedUpFactor to 1');
});
test('updateState with speedUpFactor=1 advances roughly real-time', () => {
const config = makeReactorConfig();
config.speedUpFactor = 1;
config.n_inlets = 1;
const reactor = new Reactor_CSTR(config);
// Set a known start time
const t0 = reactor.currentTime;
// Advance by 2 seconds real time
reactor.updateState(t0 + 2000);
// With speedUpFactor=1, simulation should have advanced ~2 seconds worth
// (not 120 seconds like with the old hardcoded 60x factor)
const elapsed = reactor.currentTime - t0;
assert.ok(elapsed < 5000, `Elapsed ${elapsed}ms should be close to 2000ms, not 120000ms (old 60x factor)`);
});

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test/basic/structure-module-load.basic.test.js
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const test = require('node:test');
const assert = require('node:assert/strict');
test('reactor module load smoke', () => {
assert.doesNotThrow(() => {
require('../../reactor.js');
});
});

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test/edge/.gitkeep
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15
test/edge/invalid-reactor-type.edge.test.js
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@@ -1,15 +0,0 @@
const test = require('node:test');
const assert = require('node:assert/strict');
const NodeClass = require('../../src/nodeClass');
const { makeNodeStub, makeUiConfig } = require('../helpers/factories');
test('_setupClass with unknown reactor_type throws (known error-path behavior)', () => {
const inst = Object.create(NodeClass.prototype);
inst.node = makeNodeStub();
inst.config = makeUiConfig({ reactor_type: 'UNKNOWN_TYPE' });
assert.throws(() => {
inst._setupClass();
});
});

30
test/edge/invalid-topic.edge.test.js
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@@ -1,30 +0,0 @@
const test = require('node:test');
const assert = require('node:assert/strict');
const NodeClass = require('../../src/nodeClass');
const { makeNodeStub, makeREDStub } = require('../helpers/factories');
test('unknown input topic does not throw and still calls done', () => {
const inst = Object.create(NodeClass.prototype);
const node = makeNodeStub();
inst.node = node;
inst.RED = makeREDStub();
inst.source = {
childRegistrationUtils: {
registerChild() {},
},
updateState() {},
};
inst._attachInputHandler();
let doneCalled = 0;
assert.doesNotThrow(() => {
node._handlers.input({ topic: 'somethingUnknown', payload: 1 }, () => {}, () => {
doneCalled += 1;
});
});
assert.equal(doneCalled, 1);
});

28
test/edge/missing-child.edge.test.js
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@@ -1,28 +0,0 @@
const test = require('node:test');
const assert = require('node:assert/strict');
const NodeClass = require('../../src/nodeClass');
const { makeNodeStub, makeREDStub } = require('../helpers/factories');
test('registerChild with unknown node id is ignored without throwing', () => {
const inst = Object.create(NodeClass.prototype);
const node = makeNodeStub();
inst.node = node;
inst.RED = makeREDStub();
inst.source = {
childRegistrationUtils: {
registerChild() {},
},
};
inst._attachInputHandler();
assert.doesNotThrow(() => {
node._handlers.input(
{ topic: 'registerChild', payload: 'missing-child', positionVsParent: 'upstream' },
() => {},
() => {},
);
});
});

16
test/edge/pfr-measurement-grid.edge.test.js
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@@ -1,16 +0,0 @@
const test = require('node:test');
const assert = require('node:assert/strict');
const { Reactor_PFR } = require('../../src/specificClass');
const { makeReactorConfig } = require('../helpers/factories');
test('oxygen measurement at exact reactor length is clamped to the last PFR grid index', () => {
const reactor = new Reactor_PFR(
makeReactorConfig({ reactor_type: 'PFR', length: 10, resolution_L: 5, n_inlets: 1 }),
);
assert.doesNotThrow(() => {
reactor._updateMeasurement('quantity (oxygen)', 2.5, 10, {});
});
assert.equal(reactor.state[reactor.n_x - 1][0], 2.5);
});

11
test/edge/structure-examples-node-type.edge.test.js
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@@ -1,11 +0,0 @@
const test = require('node:test');
const assert = require('node:assert/strict');
const fs = require('node:fs');
const path = require('node:path');
const flow = JSON.parse(fs.readFileSync(path.resolve(__dirname, '../../examples/basic.flow.json'), 'utf8'));
test('basic example includes node type reactor', () => {
const count = flow.filter((n) => n && n.type === 'reactor').length;
assert.equal(count >= 1, true);
});

27
test/edge/zero-dispersion.edge.test.js
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const test = require('node:test');
const assert = require('node:assert/strict');
const { Reactor_PFR } = require('../../src/specificClass');
const { makeReactorConfig } = require('../helpers/factories');
const DAY_MS = 1000 * 60 * 60 * 24;
test('updateState warns when local Peclet number is too high at zero dispersion', () => {
const reactor = new Reactor_PFR(
makeReactorConfig({ reactor_type: 'PFR', length: 10, resolution_L: 5, volume: 50, n_inlets: 1 }),
);
const warnings = [];
reactor.logger.warn = (msg) => warnings.push(String(msg));
reactor.currentTime = 0;
reactor.timeStep = 1;
reactor.speedUpFactor = 1;
reactor.Fs[0] = 2;
reactor.D = 0;
reactor.tick = () => reactor.state;
reactor.updateState(DAY_MS);
assert.equal(warnings.some((w) => w.includes('Péclet number') || w.includes('Peclet number')), true);
});

0
test/helpers/.gitkeep
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149
test/helpers/factories.js
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@@ -1,149 +0,0 @@
const EventEmitter = require('node:events');
function makeUiConfig(overrides = {}) {
return {
name: 'reactor-test',
reactor_type: 'CSTR',
volume: 100,
length: 10,
resolution_L: 5,
alpha: 0,
n_inlets: 1,
kla: NaN,
S_O_init: 0,
S_I_init: 30,
S_S_init: 100,
S_NH_init: 16,
S_N2_init: 0,
S_NO_init: 0,
S_HCO_init: 5,
X_I_init: 25,
X_S_init: 75,
X_H_init: 30,
X_STO_init: 0,
X_A_init: 0.001,
X_TS_init: 125,
timeStep: 1,
enableLog: false,
logLevel: 'error',
positionVsParent: 'atEquipment',
...overrides,
};
}
function makeReactorConfig(overrides = {}) {
const ui = makeUiConfig(overrides);
return {
general: {
id: 'reactor-node-1',
name: ui.name,
unit: null,
logging: {
enabled: ui.enableLog,
logLevel: ui.logLevel,
},
},
functionality: {
positionVsParent: ui.positionVsParent || 'atEquipment',
softwareType: 'reactor',
},
reactor_type: ui.reactor_type,
volume: Number(ui.volume),
length: Number(ui.length),
resolution_L: Number(ui.resolution_L),
alpha: Number(ui.alpha),
n_inlets: Number(ui.n_inlets),
kla: Number(ui.kla),
initialState: [
Number(ui.S_O_init),
Number(ui.S_I_init),
Number(ui.S_S_init),
Number(ui.S_NH_init),
Number(ui.S_N2_init),
Number(ui.S_NO_init),
Number(ui.S_HCO_init),
Number(ui.X_I_init),
Number(ui.X_S_init),
Number(ui.X_H_init),
Number(ui.X_STO_init),
Number(ui.X_A_init),
Number(ui.X_TS_init),
],
timeStep: Number(ui.timeStep),
};
}
function makeNodeStub() {
const handlers = {};
const sent = [];
const warns = [];
const errors = [];
const statuses = [];
return {
id: 'reactor-node-1',
source: null,
on(event, cb) {
handlers[event] = cb;
},
send(msg) {
sent.push(msg);
},
warn(msg) {
warns.push(msg);
},
error(msg) {
errors.push(msg);
},
status(msg) {
statuses.push(msg);
},
_handlers: handlers,
_sent: sent,
_warns: warns,
_errors: errors,
_statuses: statuses,
};
}
function makeREDStub(nodeMap = {}) {
return {
nodes: {
getNode(id) {
return nodeMap[id] || null;
},
createNode() {},
registerType() {},
},
httpAdmin: {
get() {},
},
};
}
function makeMeasurementChild({
id = 'measurement-1',
name = 'temp-sensor-1',
distance = 'atEquipment',
positionVsParent = 'atEquipment',
type = 'temperature',
} = {}) {
return {
config: {
general: { id, name },
functionality: { distance, positionVsParent, softwareType: 'measurement' },
asset: { type },
},
measurements: {
emitter: new EventEmitter(),
},
};
}
module.exports = {
makeUiConfig,
makeReactorConfig,
makeNodeStub,
makeREDStub,
makeMeasurementChild,
};

0
test/integration/.gitkeep
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26
test/integration/measurement-temperature.integration.test.js
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@@ -1,26 +0,0 @@
const test = require('node:test');
const assert = require('node:assert/strict');
const { Reactor_CSTR } = require('../../src/specificClass');
const { makeReactorConfig, makeMeasurementChild } = require('../helpers/factories');
test('measurement child temperature event updates reactor temperature', () => {
const reactor = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR' }));
const measurement = makeMeasurementChild({
type: 'temperature',
distance: 'atEquipment',
positionVsParent: 'upstream',
});
reactor.registerChild(measurement, 'measurement');
measurement.measurements.emitter.emit('temperature.measured.atEquipment', {
childName: 'T-1',
value: 27.5,
unit: 'C',
timestamp: Date.now(),
});
assert.equal(reactor.temperature, 27.5);
});

91
test/integration/otr-kla.integration.test.js
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@@ -1,91 +0,0 @@
const test = require('node:test');
const assert = require('node:assert/strict');
const { Reactor_CSTR, Reactor_PFR } = require('../../src/specificClass');
const { makeReactorConfig } = require('../helpers/factories');
const NUM_SPECIES = 13;
test('CSTR uses external OTR when kla is NaN', () => {
const reactor = new Reactor_CSTR(
makeReactorConfig({ reactor_type: 'CSTR', kla: NaN, n_inlets: 1 }),
);
reactor.asm = {
compute_dC: () => Array(NUM_SPECIES).fill(0),
};
reactor.Fs[0] = 0;
reactor.OTR = 4;
reactor.state = Array(NUM_SPECIES).fill(0);
reactor.tick(1);
assert.equal(reactor.state[0], 4);
});
test('CSTR uses kla-based oxygen transfer when kla is finite', () => {
const reactor = new Reactor_CSTR(
makeReactorConfig({ reactor_type: 'CSTR', kla: 2, n_inlets: 1 }),
);
reactor.asm = {
compute_dC: () => Array(NUM_SPECIES).fill(0),
};
reactor.Fs[0] = 0;
reactor.OTR = 1;
reactor.state = Array(NUM_SPECIES).fill(0);
const expected = Math.min(
reactor._calcOTR(0, reactor.temperature),
reactor._calcOxygenSaturation(reactor.temperature),
);
reactor.tick(1);
assert.ok(Math.abs(reactor.state[0] - expected) < 1e-9);
});
test('PFR uses external OTR branch when kla is NaN', () => {
const reactor = new Reactor_PFR(
makeReactorConfig({ reactor_type: 'PFR', kla: NaN, n_inlets: 1, length: 8, resolution_L: 6, volume: 40 }),
);
reactor.asm = {
compute_dC: () => Array(NUM_SPECIES).fill(0),
};
reactor.Fs[0] = 0;
reactor.D = 0;
reactor.OTR = 3;
reactor.state = Array.from({ length: reactor.n_x }, () => Array(NUM_SPECIES).fill(0));
reactor.tick(1);
assert.equal(reactor.state[1][0], 4.5);
assert.equal(reactor.state[2][0], 4.5);
assert.equal(reactor.state[3][0], 4.5);
assert.equal(reactor.state[4][0], 4.5);
});
test('PFR uses kla-based transfer branch when kla is finite', () => {
const reactor = new Reactor_PFR(
makeReactorConfig({ reactor_type: 'PFR', kla: 1, n_inlets: 1, length: 8, resolution_L: 6, volume: 40 }),
);
reactor.asm = {
compute_dC: () => Array(NUM_SPECIES).fill(0),
};
reactor.Fs[0] = 0;
reactor.D = 0;
reactor.OTR = 0;
reactor.state = Array.from({ length: reactor.n_x }, () => Array(NUM_SPECIES).fill(0));
const expected = Math.min(
reactor._calcOTR(0, reactor.temperature) * (reactor.n_x / (reactor.n_x - 2)),
reactor._calcOxygenSaturation(reactor.temperature),
);
reactor.tick(1);
assert.ok(Math.abs(reactor.state[1][0] - expected) < 1e-9);
assert.ok(Math.abs(reactor.state[2][0] - expected) < 1e-9);
assert.ok(Math.abs(reactor.state[3][0] - expected) < 1e-9);
assert.ok(Math.abs(reactor.state[4][0] - expected) < 1e-9);
});

35
test/integration/pfr-boundary.integration.test.js
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@@ -1,35 +0,0 @@
const test = require('node:test');
const assert = require('node:assert/strict');
const { Reactor_PFR } = require('../../src/specificClass');
const { makeReactorConfig } = require('../helpers/factories');
test('_applyBoundaryConditions enforces Danckwerts inlet and Neumann outlet for flowing case', () => {
const reactor = new Reactor_PFR(
makeReactorConfig({ reactor_type: 'PFR', n_inlets: 1, length: 10, resolution_L: 5, volume: 50, alpha: 0.2 }),
);
reactor.Fs[0] = 2;
reactor.Cs_in[0] = Array(13).fill(9);
reactor.D = 1;
const state = Array.from({ length: reactor.n_x }, (_, i) => Array(13).fill(i));
reactor._applyBoundaryConditions(state);
assert.deepEqual(state[reactor.n_x - 1], state[reactor.n_x - 2]);
assert.equal(state[0].every((v) => Number.isFinite(v)), true);
});
test('_applyBoundaryConditions copies first interior slice when no flow is present', () => {
const reactor = new Reactor_PFR(
makeReactorConfig({ reactor_type: 'PFR', n_inlets: 1, length: 10, resolution_L: 5, volume: 50 }),
);
reactor.Fs[0] = 0;
const state = Array.from({ length: reactor.n_x }, (_, i) => Array(13).fill(i + 10));
reactor._applyBoundaryConditions(state);
assert.deepEqual(state[0], state[1]);
assert.deepEqual(state[reactor.n_x - 1], state[reactor.n_x - 2]);
});

23
test/integration/structure-examples.integration.test.js
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@@ -1,23 +0,0 @@
const test = require('node:test');
const assert = require('node:assert/strict');
const fs = require('node:fs');
const path = require('node:path');
const dir = path.resolve(__dirname, '../../examples');
function loadJson(file) {
return JSON.parse(fs.readFileSync(path.join(dir, file), 'utf8'));
}
test('examples package exists for reactor', () => {
for (const file of ['README.md', 'basic.flow.json', 'integration.flow.json', 'edge.flow.json']) {
assert.equal(fs.existsSync(path.join(dir, file)), true, file + ' missing');
}
});
test('example flows are parseable arrays for reactor', () => {
for (const file of ['basic.flow.json', 'integration.flow.json', 'edge.flow.json']) {
const parsed = loadJson(file);
assert.equal(Array.isArray(parsed), true);
}
});

134
test/integration/tick-loop.integration.test.js
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@@ -1,134 +0,0 @@
const test = require('node:test');
const assert = require('node:assert/strict');
const NodeClass = require('../../src/nodeClass');
const { makeNodeStub } = require('../helpers/factories');
test('_tick emits source effluent on process output', () => {
const inst = Object.create(NodeClass.prototype);
const node = makeNodeStub();
inst.node = node;
inst._output = { formatMsg() { return null; } };
inst.source = {
get getEffluent() {
return { topic: 'Fluent', payload: { inlet: 0, F: 1, C: [] }, timestamp: 1 };
},
};
inst._tick();
assert.equal(node._sent.length, 1);
assert.equal(node._sent[0][0].topic, 'Fluent');
assert.equal(node._sent[0][1], null);
assert.equal(node._sent[0][2], null);
});
test('_tick emits reactor telemetry on influx output', () => {
const inst = Object.create(NodeClass.prototype);
const node = makeNodeStub();
let captured = null;
inst.node = node;
inst.config = { functionality: { softwareType: 'reactor' }, general: { id: 'reactor-node-1' } };
inst._output = {
formatMsg(output, config, format) {
captured = { output, config, format };
return { topic: 'reactor_reactor-node-1', payload: { measurement: 'reactor_reactor-node-1', fields: output } };
}
};
inst.source = {
temperature: 19.5,
get getGridProfile() {
return null;
},
get getEffluent() {
return {
topic: 'Fluent',
payload: {
inlet: 0,
F: 42,
C: [2.1, 30, 100, 16, 0, 1, 8, 25, 75, 1500, 0, 15, 2500]
},
timestamp: 1
};
},
};
inst._tick();
assert.equal(node._sent.length, 1);
assert.equal(node._sent[0][0].topic, 'Fluent');
assert.equal(node._sent[0][1].topic, 'reactor_reactor-node-1');
assert.equal(captured.format, 'influxdb');
assert.equal(captured.output.flow_total, 42);
assert.equal(captured.output.temperature, 19.5);
assert.equal(captured.output.S_O, 2.1);
assert.equal(captured.output.S_NH, 16);
assert.equal(captured.output.X_TS, 2500);
});
test('_startTickLoop schedules periodic tick after startup delay', () => {
const inst = Object.create(NodeClass.prototype);
const delays = [];
const intervals = [];
let tickCount = 0;
inst._tick = () => {
tickCount += 1;
};
const originalSetTimeout = global.setTimeout;
const originalSetInterval = global.setInterval;
global.setTimeout = (fn, ms) => {
delays.push(ms);
fn();
return 10;
};
global.setInterval = (fn, ms) => {
intervals.push(ms);
fn();
return 22;
};
try {
inst._startTickLoop();
} finally {
global.setTimeout = originalSetTimeout;
global.setInterval = originalSetInterval;
}
assert.deepEqual(delays, [1000]);
assert.deepEqual(intervals, [1000]);
assert.equal(inst._tickInterval, 22);
assert.equal(tickCount, 1);
});
test('_attachCloseHandler clears tick interval and calls done callback', () => {
const inst = Object.create(NodeClass.prototype);
const node = makeNodeStub();
inst.node = node;
inst._tickInterval = 55;
const cleared = [];
const originalClearInterval = global.clearInterval;
global.clearInterval = (id) => {
cleared.push(id);
};
let doneCalled = 0;
try {
inst._attachCloseHandler();
node._handlers.close(() => {
doneCalled += 1;
});
} finally {
global.clearInterval = originalClearInterval;
}
assert.deepEqual(cleared, [55]);
assert.equal(doneCalled, 1);
});

48
test/integration/upstream-reactor.integration.test.js
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@@ -1,48 +0,0 @@
const test = require('node:test');
const assert = require('node:assert/strict');
const { Reactor_CSTR } = require('../../src/specificClass');
const { makeReactorConfig } = require('../helpers/factories');
const DAY_MS = 1000 * 60 * 60 * 24;
test('registering upstream reactor subscribes to upstream stateChange events', () => {
const downstream = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR' }));
const upstream = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR' }));
let calledWith = null;
downstream.updateState = (timestamp) => {
calledWith = timestamp;
};
downstream.registerChild(upstream, 'reactor');
upstream.emitter.emit('stateChange', 12345);
assert.equal(downstream.upstreamReactor, upstream);
assert.equal(calledWith, 12345);
});
test('updateState pulls influent from upstream reactor effluent when linked', () => {
const downstream = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR', n_inlets: 1, timeStep: 1 }));
const upstream = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR', n_inlets: 1 }));
upstream.Fs[0] = 3;
upstream.state = Array(13).fill(11);
downstream.upstreamReactor = upstream;
downstream.currentTime = 0;
downstream.timeStep = 1;
downstream.speedUpFactor = 1;
let ticks = 0;
downstream.tick = () => {
ticks += 1;
return downstream.state;
};
downstream.updateState(DAY_MS);
assert.equal(ticks, 1);
assert.equal(downstream.Fs[0], 3);
assert.deepEqual(downstream.Cs_in[0], Array(13).fill(11));
});